diff --git a/Documentation/MassBankRecordFormat.md b/Documentation/MassBankRecordFormat.md index d2a85b5e..b3134212 100644 --- a/Documentation/MassBankRecordFormat.md +++ b/Documentation/MassBankRecordFormat.md @@ -2,7 +2,7 @@ MassBank Consortium (May 13, 2022) #### Updated -- **May 2022**: With version 2.6.0 MassBank introduces a new ACCESSION scheme.ch offers more freedom for contributors in the naming of their records. The new scheme consists of three fields separated by 'minus' signs and follows the format ID-[A-Z0–9_]{1,32}-[A-Z0–9_]{1,64}. The field ID will always be MSBNK for official MassBank releases. The second field is the contributor ID and is usually assigned by MassBank staff. Now it can be up to 32 characters long and is comprised of letters, digits and the '_' sign. The third field is the ID assigned by the contributor and can be up to 64 characters long and is also comprised of letters, digits and the '_' sign. +- **May 2022**: With version 2.6.0 MassBank introduces a new ACCESSION scheme. It offers more freedom for contributors in the naming of their records. The new scheme consists of three fields separated by 'minus' signs and follows the format ID-[A-Z0–9_]{1,32}-[A-Z0–9_]{1,64}. The field ID will always be MSBNK for official MassBank releases. The second field is the contributor ID and is usually assigned by MassBank staff. Now it can be up to 32 characters long and is comprised of letters, digits and the '_' sign. The third field is the ID assigned by the contributor and can be up to 64 characters long and is also comprised of letters, digits and the '_' sign. - **July 2021**: Move to a semantic versioning scheme X.Y.Z with Z increases for changes in the description or fixing of typos, Y increases for changes that also change the Validator software and X increases with changes that break compatibility with older versions of the software. - **March 2020**: Add new tag for the inlet type. - **October 2019**: Add UVPD dissociation method and some undocumented or new tags. @@ -26,13 +26,19 @@ Multiple line information: Last line of a MassBank Record is `//`. +#### Controled Vocabulary terms +General format is `[CV label, accession, name, value]`. Any field that is not available MUST be left empty. Should the name contain commas, quotes MUST be added to avoid problems with parsing. +Example: +``` +[CV label, accession, name, value] +[MS, MS:1000443, Mass Analyzer Type, Orbitrap] +[MS, MS:1001477, SpectraST,] +[label, accession, “first part of the param name, second part of the name”, value] +``` + ### 1.2 Order of Information MassBank Record Information in a MassBank Record is arranged in a fixed order (see Section 2). -### 1.3 Others -`[MS : space value ]` is the HUPO-PSI ID in [OLS](https://www.ebi.ac.uk/ols/index). - - ## Table 1. MassBank Record Format (Summary) @@ -758,8 +764,7 @@ Example: ``` AC$MASS_SPECTROMETRY: ION_MODE POSITIVE ``` - -Either of POSITIVE or NEGATIVE is allowed. Cross-reference to HUPO-PSI: POSITIVE [MS:1000030] or NEGATIVE [MS:1000129]; Ion mode [MS:1000465] +Either of POSITIVE or NEGATIVE is allowed. Cross-reference to HUPO-PSI: POSITIVE [MS, MS:1000130, positive scan,] or NEGATIVE [MS:1000129, negative scan,]; ION_MODE [MS, MS:1000465, scan polarity,] #### 2.4.5 AC$MASS\_SPECTROMETRY: subtag Description Other Optional Experimental Methods and Conditions of Mass Spectrometry. @@ -1372,13 +1377,13 @@ Types currently used in MassBank are: [2M-H-C6H10O5]- ``` -##### 2.5.1 Subtag: PRECURSOR\_INT +##### 2.5.1 Subtag: PRECURSOR\_INTENSITY Intensity of Focused Ion. Example: ``` -MS$FOCUSED_ION: PRECURSOR_INT 10000 +MS$FOCUSED_ION: PRECURSOR_INTENSITY 10000 ``` ##### 2.5.1 Subtag: PRECURSOR\_M/Z diff --git a/MassBank-Project/MassBank-OpenAPI/pom.xml b/MassBank-Project/MassBank-OpenAPI/pom.xml index fa73c562..da376b85 100644 --- a/MassBank-Project/MassBank-OpenAPI/pom.xml +++ b/MassBank-Project/MassBank-OpenAPI/pom.xml @@ -3,7 +3,7 @@ de.ipb-halle.msbi MassBank-Project - 2.2 + 2.2.2 MassBank-OpenAPI @@ -113,7 +113,7 @@ org.springframework.boot spring-boot-dependencies - 2.7.0 + ${spring-boot.version} pom import diff --git a/MassBank-Project/MassBank-lib/pom.xml b/MassBank-Project/MassBank-lib/pom.xml index 3ed62e3a..674a03f6 100644 --- a/MassBank-Project/MassBank-lib/pom.xml +++ b/MassBank-Project/MassBank-lib/pom.xml @@ -1,9 +1,11 @@ - + 4.0.0 MassBank-Project de.ipb-halle.msbi - 2.2 + 2.2.2 MassBank-lib @@ -85,6 +87,11 @@ io.github.dan2097 jna-inchi-all + + net.sourceforge.owlapi + owlapi-distribution + 5.5.0 + org.junit.jupiter junit-jupiter-engine diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/CVUtil.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/CVUtil.java new file mode 100644 index 00000000..f4b0c4fd --- /dev/null +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/CVUtil.java @@ -0,0 +1,139 @@ +package massbank; + +import java.io.BufferedReader; +import java.io.File; +import java.io.IOException; +import java.io.InputStreamReader; +import java.net.URISyntaxException; +import java.net.URL; +import java.text.ParseException; +import java.util.ArrayList; +import java.util.Set; + +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.reasoner.BufferingMode; +import org.semanticweb.owlapi.reasoner.InferenceType; +import org.semanticweb.owlapi.reasoner.OWLReasoner; +import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; +import org.semanticweb.owlapi.reasoner.SimpleConfiguration; +import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner; +import org.semanticweb.owlapi.reasoner.NodeSet; +import org.semanticweb.owlapi.model.OWLClass; + + +/** + * Controled vocabulary handler. + * + * @author rmeier + * @version 07-10-2022 + */ +public final class CVUtil { + private static CVUtil instance; + private static Object mutex = new Object(); + //Ontology ontology; + + private CVUtil(){ +// try (BufferedReader reader = new BufferedReader(new InputStreamReader(getClass().getClassLoader().getResourceAsStream("cv/psi-ms.obo")))) { +// OboParser parser = new OboParser(); +// try { +// ontology = parser.parseOBO(reader, "Mass spectrometry ontology", "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry."); +// } catch (ParseException ex) { +// System.err.println("Parsing exception: " + ex.getLocalizedMessage()); +// } +// } catch (IOException e) { +// e.printStackTrace(); +// } +// OWLOntologyManager man = OWLManager.createOWLOntologyManager(); +// OWLOntology o=null; +// try { +// o = man.loadOntology(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl")); +// o = man.loadOntologyFromOntologyDocument(getClass().getClassLoader().getResourceAsStream("cv/psi-ms.owl")); +// } catch (OWLOntologyCreationException e) { +// // TODO Auto-generated catch block +// e.printStackTrace(); +// } +// for(OWLAxiom ax:o.getLogicalAxioms()) { +// System.out.println(ax); +// } +// System.out.println("Axioms: "+o.getAxiomCount()+", Format:"+man.getOntologyFormat(o)); +// ArrayList t = new ArrayList(); +// for(OWLClass ax:o.getClassesInSignature()) { +// t.add(ax); +// System.out.println(ax.getIRI()); +// } + + +// o.signature().filter((e->(!e.isBuiltIn()&&e.getIRI().getFragment().startsWith("M")))); + //o.signature().filter((e->(!e.isBuiltIn()&&e.getIRI().getFragment().startsWith("M")))).forEach(System.out::println); +// System.out.println(o); + //OWLReasonerFactory rf = new ReasonerFactory(); + //OWLReasoner r = rf.createReasoner(o); +// +// OWLDataFactory df = man.getOWLDataFactory(); +// OWLReasoner r = new StructuralReasoner(o, new SimpleConfiguration(),BufferingMode.BUFFERING); +// System.out.println(df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MS_1000044")).getEntityType()); +// System.out.println(df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MS_1000044")).getIRI()); +// //NodeSet result = r.getSuperClasses(df.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/pizza/pizza.owl#Hot")), false); +// NodeSet result = r.getSuperClasses(df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MS_1000044")), true); +// System.out.println(result); +// ((StructuralReasoner) r).dumpClassHierarchy(false); +// r.precomputeInferences(InferenceType.CLASS_HIERARCHY); +// r.getSubClasses(df.getOWLClass("http://purl.obolibrary.org/obo/MS:1000044"), false).forEach(System.out::println); + } + + public static CVUtil get(){ + CVUtil result = instance; + if (result == null) { + synchronized (mutex) { + result = instance; + if (result == null) + instance = result = new CVUtil(); + } + } + return result; + } + +// public boolean containsTerm(String name) { +// return ontology.containsTerm(name); +// } +// +// public Term getTerm(String name) { +// Term term = ontology.getTerm(name); +// return term; +// } + + public boolean termIsA(String name, String isA) { +// Term term = ontology.getTerm(name); +// Set keys = ontology.getTerms(); +// System.out.println(keys.toString()); +// System.out.println(term.getName()); +// System.out.println(term.getDescription()); +// System.out.println(term.getAnnotation()); +// System.out.println(term.getSynonyms().toString()); +// System.out.println(term.getOntology()); +// System.out.println(term.getOntology()); +// +// System.out.println(ontology.getTriples(ontology.getTerm("MS:1003294"), ontology.getTerm("MS:1000250") , ontology.getTerm(IS_A))); +// System.out.println(ontology.getTriples(ontology.getTerm("MS:1000250"), ontology.getTerm("MS:1003294") , ontology.getTerm(IS_A))); +// System.out.println(ontology.getTriples(ontology.getTerm("MS:1003294"), ontology.getTerm("MS:1000044") , ontology.getTerm(IS_A))); +// System.out.println(ontology.getTerm("MS:1003294").getAnnotation()); +// + +// assertTrue(getAnnotationForTerm(ontology).containsProperty(NAMESPACE)); +// assertEquals("sequence", getAnnotationForTerm(ontology).getProperty(NAMESPACE)); +// getAnnotationForTerm(ontology).getProperty(NAMESPACE) +// //(List) getAnnotationForTerm(ontology).getProperty(ALT_ID); + + + + + return true; + } + +} diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/Record.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/Record.java index c17e1d08..a433239a 100644 --- a/MassBank-Project/MassBank-lib/src/main/java/massbank/Record.java +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/Record.java @@ -21,6 +21,7 @@ package massbank; import java.math.BigDecimal; +import java.time.Instant; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; @@ -44,18 +45,25 @@ import org.openscience.cdk.silent.SilentChemObjectBuilder; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; + +import com.google.gson.Gson; +import com.google.gson.GsonBuilder; +import com.google.gson.JsonArray; +import com.google.gson.JsonObject; + import io.github.dan2097.jnainchi.InchiStatus; /** * This class keeps all data of a record. * @author rmeier - * @version 05-05-2020 + * @version 01-12-2022 */ public class Record { private static final Logger logger = LogManager.getLogger(Record.class); private String contributor; private String ACCESSION; + private Instant timestamp; private boolean deprecated; private String deprecated_content; private List RECORD_TITLE; @@ -65,9 +73,9 @@ public class Record { private String COPYRIGHT; // optional private String PUBLICATION; // optional private String PROJECT; // optional - private List COMMENT = new ArrayList();; // optional + private List COMMENT = new ArrayList(); // optional private List CH$NAME; - private List CH$COMPOUND_CLASS; + private List CH$COMPOUND_CLASS; // optional private String CH$FORMULA; private BigDecimal CH$EXACT_MASS; private String CH$SMILES; @@ -143,6 +151,14 @@ public void ACCESSION(String value) { } + public Instant getTimestamp() { + return timestamp; + } + public void setTimestamp(Instant value) { + timestamp = value; + } + + public boolean DEPRECATED() { return deprecated; } @@ -481,7 +497,9 @@ public String toString() { for (String ch_name : CH_NAME()) sb.append("CH$NAME: " + ch_name + "\n"); - sb.append("CH$COMPOUND_CLASS: " + String.join("; ", CH_COMPOUND_CLASS()) + "\n"); + if (!CH_COMPOUND_CLASS().isEmpty()) { + sb.append("CH$COMPOUND_CLASS: " + String.join("; ", CH_COMPOUND_CLASS()) + "\n"); + } sb.append("CH$FORMULA: " + CH_FORMULA() + "\n"); sb.append("CH$EXACT_MASS: " + CH_EXACT_MASS() + "\n"); sb.append("CH$SMILES: " + CH_SMILES() + "\n"); @@ -680,44 +698,6 @@ public String createRecordString() { return sb.toString(); } - public class MolecularEntity { - String identifier; - String url; - String name; - List alternateName; - String inchikey; - String description; - String molecularFormula; - - - MolecularEntity( - String identifier, - String url, - String name, - List alternateName, - String inchikey, - String description, - String molecularFormula - ) - { - this.identifier=identifier; - this.url=url; - this.name=name; - this.alternateName=alternateName; - this.inchikey=inchikey; - this.description=description; - this.molecularFormula=molecularFormula; - } - } - -// sb.append("\"molecularFormula\": \""+CH_FORMULA()+"\",\n"); -// sb.append("\"monoisotopicMolecularWeight\": \""+CH_EXACT_MASS()+"\",\n"); -// sb.append("\"inChI\": \""+CH_IUPAC()+"\",\n"); -// sb.append("\"smiles\": \""+CH_SMILES()+"\",\n"); -// sb.append("\"@context\": \"http://schema.org\",\n"); -// sb.append("\"@type\": \"MolecularEntity\"\n"); -// sb.append("},\n"); - // [ // { // "identifier": "LQB00001", @@ -767,78 +747,92 @@ public class MolecularEntity { //https://github.com/BioSchemas/specifications/issues/198 - public String createStructuredData() { + public JsonArray createStructuredDataJsonArray() { + if (DEPRECATED()) { + return new JsonArray(); + } String InChiKey = CH_LINK().get("INCHIKEY"); String description = "This MassBank record with Accession " + ACCESSION() + " contains the " + AC_MASS_SPECTROMETRY_MS_TYPE() + " mass spectrum of " + RECORD_TITLE().get(0) + ((InChiKey!=null) ? "." : " with the InChIkey " + InChiKey + "."); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); -// MolecularEntity molecularEntity = new MolecularEntity( -// ACCESSION(), -// "https://massbank.eu/MassBank/RecordDisplay?id="+ACCESSION(), -// RECORD_TITLE().get(0), -// CH_NAME(), -// CH_LINK().get("INCHIKEY"), -// description, -// CH_FORMULA() -// ); -// Gson gson = new GsonBuilder().setPrettyPrinting().create(); -// String molecularEntityJson = gson.toJson(molecularEntity); -// System.out.println(molecularEntityJson); + JsonObject dataset = new JsonObject(); + dataset.addProperty("@context", "https://schema.org"); + dataset.addProperty("@type", "Dataset"); + dataset.addProperty("@id", "https://massbank.eu/MassBank/RecordDisplay?id="+ACCESSION()); + dataset.add("http://purl.org/dc/terms/conformsTo", + gson.fromJson("{ \"@type\": \"CreativeWork\", \"@id\": \"https://bioschemas.org/profiles/Dataset/1.0-RELEASE\" }", JsonObject.class)); + dataset.addProperty("description", description); + dataset.addProperty("identifier", ACCESSION()); + JsonArray keywords = new JsonArray(); + keywords.add(gson.fromJson("{ \"@type\": \"DefinedTerm\", \"@id\": \"http://edamontology.org/data_2536\", \"name\": \"Mass spectrometry data\" }", JsonObject.class)); + dataset.add("keywords", keywords); + if (LICENSE().equals("CC0")) { + dataset.addProperty("license", "https://creativecommons.org/share-your-work/public-domain/cc0"); + } else if (LICENSE().equals("CC BY-SA")) { + dataset.addProperty("license", "https://creativecommons.org/licenses/by-sa/4.0"); + } else if (LICENSE().equals("CC BY")) { + dataset.addProperty("license", "https://creativecommons.org/licenses/by/4.0"); + } else if (LICENSE().equals("CC BY-NC")) { + dataset.addProperty("license", "https://creativecommons.org/licenses/by-nc/4.0"); + } else if (LICENSE().equals("CC BY-NC-SA")) { + dataset.addProperty("license", "https://creativecommons.org/licenses/by-nc-sa/4.0"); + } + dataset.addProperty("name", RECORD_TITLE1()); + dataset.addProperty("url", "https://massbank.eu/MassBank/RecordDisplay?id="+ACCESSION()); + + dataset.addProperty("datePublished", DATE1()[0].replace(".","-")); - StringBuilder sb = new StringBuilder(); - sb.append(""); - return sb.toString(); + + JsonObject molecularEntity = new JsonObject(); + molecularEntity.addProperty("@context", "https://schema.org"); + molecularEntity.addProperty("@type", "MolecularEntity"); + molecularEntity.addProperty("@id", "https://massbank.eu/MassBank/RecordDisplay?id=" + + ACCESSION() + + "#" + (InChiKey!=null ? InChiKey : "")); + molecularEntity.add("http://purl.org/dc/terms/conformsTo", + gson.fromJson("{ \"@type\": \"CreativeWork\", \"@id\": \"https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE\" }", JsonObject.class)); + + molecularEntity.addProperty("identifier", ACCESSION()); + molecularEntity.addProperty("url", "https://massbank.eu/MassBank/RecordDisplay?id="+ACCESSION()); + molecularEntity.addProperty("name", RECORD_TITLE().get(0)); + molecularEntity.addProperty("inChI", CH_IUPAC()); + molecularEntity.addProperty("smiles", CH_SMILES()); + molecularEntity.addProperty("molecularFormula", CH_FORMULA()); + molecularEntity.addProperty("description", description); + molecularEntity.addProperty("monoisotopicMolecularWeight", CH_EXACT_MASS()); + if (InChiKey!=null) molecularEntity.addProperty("inChIKey", InChiKey); + if (CH_NAME().size() == 1) molecularEntity.addProperty("alternateName", CH_NAME().get(0)); + else if (CH_NAME().size() >= 1) molecularEntity.add("alternateName", gson.toJsonTree(CH_NAME())); + + + + // put MolecularEntity and Dataset together + JsonArray structuredData = new JsonArray(); + structuredData.add(dataset); + structuredData.add(molecularEntity); + return structuredData; + } + public String createStructuredData() { + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(createStructuredDataJsonArray()); + } + + public String createPeakListForSpectrumViewer() { // convert a list of lists [[mz, int, rel.int], [...], ...] // to String "mz,rel.int@mz,rel.int@..." diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/RecordParserDefinition.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/RecordParserDefinition.java index cb3fbb38..7bb783e3 100644 --- a/MassBank-Project/MassBank-lib/src/main/java/massbank/RecordParserDefinition.java +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/RecordParserDefinition.java @@ -2,6 +2,7 @@ import static org.petitparser.parser.primitive.CharacterParser.digit; import static org.petitparser.parser.primitive.CharacterParser.letter; +import static org.petitparser.parser.primitive.CharacterParser.word; import java.io.BufferedReader; import java.io.File; @@ -63,7 +64,7 @@ public class RecordParserDefinition extends GrammarDefinition { private final boolean legacy; // weak validation mode to let validation pass for AddMetaData private final boolean weak; - // torn on additional validation steps, which require online checks + // turn on additional validation steps, which require online checks; slow! private final boolean online; private IMolecularFormula fromCH_FORMULA = SilentChemObjectBuilder.getInstance().newInstance(IMolecularFormula.class); @@ -74,7 +75,10 @@ public class RecordParserDefinition extends GrammarDefinition { private String InChiKeyFromCH_IUPAC = ""; private String InChiKeyFromCH_LINK = ""; private int pk_num_peak = -1; + // controled vocabulary handler + CVUtil cvutil = CVUtil.get(); + // load a list of strings from .config or resource folder private static List getResourceFileAsList(String fileName) { // Try to load from user DataRootPath File resourceFileFromDataRootPath = null; @@ -134,7 +138,7 @@ public RecordParserDefinition(Record callback, Set config) { .seq(ref("project").optional()) .seq(ref("comment").optional()) .seq(ref("ch_name")) - .seq(ref("ch_compound_class")) + .seq(ref("ch_compound_class").optional()) .seq(ref("ch_formula")) .seq(ref("ch_exact_mass")) .seq(ref("ch_smiles")) @@ -184,6 +188,56 @@ public RecordParserDefinition(Record callback, Set config) { def("endtag", StringParser.of("//").seq(Token.NEWLINE_PARSER)); def("multiline_start", StringParser.of(" ")); + // CV terms + // General format is [CV label, accession, name, value]. + // Any field that is not available MUST be left empty. + // [MS, MS:1001477, SpectraST,] + // Should the name of the param contain commas, quotes MUST be added to avoid problems with the parsing: + // [label, accession, “first part of the param name, second part of the name”, value]. + // [MOD, MOD:00648, "N,O-diacetylated L-serine",] + def("cvterm", + CharacterParser.of('[').trim() + // label + .seq(word().star().flatten()) + .seq(CharacterParser.of(',').trim()) + // accession + .seq(word().or(CharacterParser.of(':')).star().flatten().trim()) + .seq(CharacterParser.of(',')) + // name + .seq( + CharacterParser.of('"').seq(CharacterParser.any().plusLazy(CharacterParser.of('"'))).seq(CharacterParser.of('"')) + .or(CharacterParser.any().starLazy(CharacterParser.of(','))).flatten().trim() + ) + .seq(CharacterParser.of(',')) + // value + .seq( + CharacterParser.of('"').seq(CharacterParser.any().plusLazy(CharacterParser.of('"'))).seq(CharacterParser.of('"')) + .or(CharacterParser.any().starLazy(CharacterParser.of(']'))).flatten().trim() + ) + .seq(CharacterParser.of(']')).permute(1,3,5,7) +// .map((List value) -> { +// System.out.println(value); +// return value; +// }) + ); + def("cvterm_validated", + ref("cvterm") + .callCC((Function continuation, Context context) -> { + Result r = continuation.apply(context); + if (r.isSuccess()) { + List value = r.get(); +// if (!cvutil.containsTerm(value.get(1))) { +// return context.failure(value.get(1)+ "is no valid Id in ontology."); +// } +// Term term=cvutil.getTerm(value.get(1)); +// if (!term.getDescription().equals(value.get(2))) { +// return context.failure("Name missmatch for id "+ value.get(1)+ "."); +// } + } + return r; + }) + ); + def("uint_primitive", digit().plus().flatten()); def("number_primitive", digit().plus() @@ -213,7 +267,7 @@ public RecordParserDefinition(Record callback, Set config) { .seq(CharacterParser.of('-')) .seq(letter().or(digit()).or(CharacterParser.of('_')).repeat(1,32)) .seq(CharacterParser.of('-')) - .seq(letter().or(digit()).or(CharacterParser.of('_')).repeat(1,64)) + .seq(CharacterParser.upperCase().or(digit()).or(CharacterParser.of('_')).repeat(1,64)) .flatten() .map((String value) -> { callback.ACCESSION(value); @@ -1169,8 +1223,8 @@ else if (ret == InchiStatus.ERROR) { // 2.4.4 AC$MASS_SPECTROMETRY: ION_MODE // Polarity of Ion Detection. Mandatory // Example: AC$MASS_SPECTROMETRY: ION_MODE POSITIVE - // Either of POSITIVE or NEGATIVE is allowed. Cross-reference to mzOntology: POSITIVE [MS:1000030] - // or NEGATIVE [MS:1000129]; Ion mode [MS:1000465] + // Either of POSITIVE or NEGATIVE is allowed. + // Cross-reference to HUPO-PSI: POSITIVE [MS, MS:1000130, positive scan,] or NEGATIVE [MS:1000129, negative scan,]; ION_MODE [MS, MS:1000465, scan polarity,] def("ac_mass_spectrometry_ion_mode_value", StringParser.of("POSITIVE") .or(StringParser.of("NEGATIVE")) @@ -1249,8 +1303,6 @@ else if (ret == InchiStatus.ERROR) { .or(StringParser.of("DESOLVATION_TEMPERATURE ")) .or(StringParser.of("DRY_GAS_FLOW ")) .or(StringParser.of("DRY_GAS_TEMP ")) - .or(StringParser.of("FRAGMENTATION_METHOD ")) - .or(StringParser.of("FRAGMENTATION_MODE ")) .or(StringParser.of("FRAGMENT_VOLTAGE ")) .or(StringParser.of("GAS_PRESSURE ")) .or(StringParser.of("HELIUM_FLOW ")) @@ -1299,8 +1351,32 @@ else if (ret == InchiStatus.ERROR) { StringParser.of("AC$MASS_SPECTROMETRY") .seq(ref("tagsep")) .seq( + // tag ref("ac_mass_spectrometry_subtag") + // value + .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()) + .or( + // FRAGMENTATION_MODE [MS, MS:1000044, dissociation method,] + StringParser.of("FRAGMENTATION_MODE ") + // value + .seq( + ref("cvterm") + .map((List value) -> { +// Term term=cvutil.getTerm(value.get(1)); + return '['+String.join(", ", value)+']'; + }) + .or( + StringParser.of("CID") + .or(StringParser.of("HAD")) + .or(StringParser.of("HCD")) + .or(StringParser.of("LOW-ENERGY CID")) + .or(StringParser.of("RID")) + ) + ) + ) + .or( + // free tag CharacterParser.letter().or(CharacterParser.digit()).or(CharacterParser.of('_')).or(CharacterParser.of('/')) .plus().flatten() .map((String value) -> { @@ -1308,16 +1384,22 @@ else if (ret == InchiStatus.ERROR) { return value; }) .seq(CharacterParser.whitespace()).flatten() + // value + .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()) ) ) - .seq(Token.NEWLINE_PARSER.not()).pick(2) - .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()) + .seq(Token.NEWLINE_PARSER).pick(2) .map((List value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }) - .seq(Token.NEWLINE_PARSER).pick(0) - .plus() + +// .map((Pair value) -> { +// System.out.println(value); +// return value; +// }) + .plus() .map((List> value) -> { + //System.out.println(); //System.out.println(value); callback.AC_MASS_SPECTROMETRY(value); return value; @@ -1423,7 +1505,7 @@ else if (ret == InchiStatus.ERROR) { def("adduct_token", CharacterParser.anyOf("+-") .seq(ref("uint_primitive").optional()) - .seq( + .seq( StringParser.of("ACN") .or(StringParser.of("FA")) .or(ref("molecular_formula")) diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/Inspector.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/Inspector.java index b40271ea..69a2d3b2 100644 --- a/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/Inspector.java +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/Inspector.java @@ -9,11 +9,16 @@ import java.io.InputStreamReader; import java.nio.charset.StandardCharsets; import java.util.HashSet; +import java.util.Properties; import java.util.Set; import java.util.stream.Collectors; +import org.apache.commons.cli.CommandLine; +import org.apache.commons.cli.DefaultParser; +import org.apache.commons.cli.HelpFormatter; +import org.apache.commons.cli.Options; +import org.apache.commons.cli.ParseException; import org.apache.commons.io.FileUtils; -import org.apache.commons.lang3.tuple.Pair; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.openscience.cdk.depict.Depiction; @@ -22,15 +27,15 @@ import massbank.Record; - /** * This class converts a record file to a html file for inspection. + * * @author rmeier - * @version 01-03-2019 + * @version 02-12-2022 */ public class Inspector { private static final Logger logger = LogManager.getLogger(Inspector.class); - + static String getResourceFileAsString(String fileName) throws IOException { ClassLoader classLoader = ClassLoader.getSystemClassLoader(); try (InputStream is = classLoader.getResourceAsStream(fileName)) { @@ -41,119 +46,113 @@ static String getResourceFileAsString(String fileName) throws IOException { } } } - public static void main(String[] arguments) throws Exception { - if (arguments.length==2) { - String input = FileUtils.readFileToString(new File(arguments[0]), StandardCharsets.UTF_8); - Validator.hasNonStandardChars(input); - Set config = new HashSet(); - config.add("legacy"); - Record record = Validator.validate(input, config); - if (record == null) { - logger.error("Error in " + arguments[0]+ ". Exiting..."); - System.exit(1); - } - else { - logger.trace("Validation passed for " + arguments[0] + "."); - } - + // load version and print + final Properties properties = new Properties(); + try { + properties.load(ClassLoader.getSystemClassLoader().getResourceAsStream("project.properties")); + } catch (IOException e) { + e.printStackTrace(); + System.exit(1); + } + System.out.println("Inspector version: " + properties.getProperty("version")); + + // parse command line + Options options = new Options(); + options.addOption(null, "only-jsonld", false, "only output structured data in JSON+LD format to file."); + CommandLine cmd = null; + try { + cmd = new DefaultParser().parse(options, arguments); + } catch (ParseException e) { + // oops, something went wrong + System.err.println("Parsing command line failed. Reason: " + e.getMessage()); + HelpFormatter formatter = new HelpFormatter(); + formatter.printHelp("Inspector [OPTIONS] ", options); + System.exit(1); + } + if (cmd.getArgList().size() != 2) { + HelpFormatter formatter = new HelpFormatter(); + formatter.printHelp("Inspector [OPTIONS] ", options); + System.exit(1); + } + + String input = FileUtils.readFileToString(new File(cmd.getArgList().get(0)), StandardCharsets.UTF_8); + Validator.hasNonStandardChars(input); + Set config = new HashSet(); + config.add("legacy"); + Record record = Validator.validate(input, config); + if (record == null) { + logger.error("Error in " + arguments[0] + ". Exiting..."); + System.exit(1); + } else { + logger.trace("Validation passed for " + arguments[0] + "."); + } + + StringBuilder sb = new StringBuilder(); + if (cmd.hasOption("only-jsonld")) { + sb.append(record.createStructuredData()); + } else { String accession = record.ACCESSION(); - String shortname = record.RECORD_TITLE().get(0)+ " Mass Spectrum"; + String shortname = record.RECORD_TITLE().get(0) + " Mass Spectrum"; // find InChIKey in CH_LINK String inchikey = record.CH_LINK().get("INCHIKEY"); - String keywords = - accession + ", " - + shortname +", " - + (inchikey != null ? inchikey + ", " : "") - + "mass spectrum, MassBank record, mass spectrometry, mass spectral library"; - String description = - "This MassBank Record with Accession " + accession + - " contains the " + record.AC_MASS_SPECTROMETRY_MS_TYPE() + " mass spectrum" + - " of '" + record.RECORD_TITLE().get(0) + "'" + - (inchikey != null ? " with the InChIKey '" + inchikey + "'" : "") + - "."; + String keywords = accession + ", " + shortname + ", " + (inchikey != null ? inchikey + ", " : "") + + "mass spectrum, MassBank record, mass spectrometry, mass spectral library"; + String description = "This MassBank Record with Accession " + accession + " contains the " + + record.AC_MASS_SPECTROMETRY_MS_TYPE() + " mass spectrum" + " of '" + record.RECORD_TITLE().get(0) + + "'" + (inchikey != null ? " with the InChIKey '" + inchikey + "'" : "") + "."; String recordstring = record.createRecordString(); String structureddata = record.createStructuredData(); IAtomContainer mol = record.CH_SMILES_obj(); - String svg = new DepictionGenerator().withAtomColors().depict(mol).toSvgStr(Depiction.UNITS_PX); - - - String css = "\n"; - - String js = "\n"; - - - StringBuilder sb = new StringBuilder(); - sb.append( - "\n" + - "\n" + - "\n" + - " "+shortname+"\n" + - " \n" + - " \n" + + String svg = new DepictionGenerator().withAtomColors().depict(mol).toSvgStr(Depiction.UNITS_PX); + + String css = "\n"; + + String js = "\n"; + + sb.append("\n" + "\n" + "\n" + " " + shortname + "\n" + + " \n" + + " \n" + // " \n" + // " \n" + - " \n" + - - " \n" + - " \n" + - " \n" + - - structureddata + "\n" + - css + "\n" + - "\n" - ); - - sb.append( - "\n" + - js + "\n" + - "
\n" + - "
\n" + - "
\n" + - "

\n" + - " MassBank Record: "+ accession + "\n" + - "

\n" + - "
\n" + - "
\n" + - "

" + record.RECORD_TITLE1() +"

\n" + - "
\n" + - "
\n" + - " Mass Spectrum\n" + - "
\n" + - "
\n" + - "
\n" + - " Chemical Structure
\n" + - svg + "\n" + - "
\n" + - "
\n" + - "
\n" + - - "
\n" + - "
\n" + - recordstring +"\n" + - "
\n" + - "\n" + - "" - ); - - File file = new File(arguments[1]); - try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) { - writer.write(sb.toString()); - } - + " \n" + + + " \n" + + " \n" + + " \n" + + "\n" + + css + "\n" + "\n"); + + sb.append("\n" + js + "\n" + + "
\n" + + "
\n" + "
\n" + "

\n" + + " MassBank Record: " + accession + "\n" + "

\n" + + "
\n" + "
\n" + "

" + + record.RECORD_TITLE1() + "

\n" + "
\n" + + "
\n" + + " Mass Spectrum\n" + "
\n" + + "
\n" + + "
\n" + + " Chemical Structure
\n" + svg + "\n" + "
\n" + + "
\n" + "
\n" + + + "
\n" + + "
\n" + recordstring + "\n" + "
\n" + "\n" + ""); } - else { - logger.error("Input and output file required. Exiting..."); + + File file = new File(cmd.getArgList().get(1)); + try (BufferedWriter writer = new BufferedWriter(new FileWriter(file))) { + writer.write(sb.toString()); } + } } diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/Msbnk2JSONLD.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/Msbnk2JSONLD.java new file mode 100644 index 00000000..f1e9dde8 --- /dev/null +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/Msbnk2JSONLD.java @@ -0,0 +1,163 @@ +package massbank.cli; + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashSet; +import java.util.List; +import java.util.Objects; +import java.util.Properties; +import java.util.Set; +import java.util.concurrent.atomic.AtomicBoolean; +import java.util.stream.Collectors; +import org.apache.commons.cli.CommandLine; +import org.apache.commons.cli.DefaultParser; +import org.apache.commons.cli.HelpFormatter; +import org.apache.commons.cli.Options; +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.FilenameUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.petitparser.context.Result; + +import com.google.gson.Gson; +import com.google.gson.GsonBuilder; +import com.google.gson.JsonArray; + +import massbank.Record; +import massbank.RecordParser; + +/** + * This class creates a JSON+LD structured data file for all records given. + * @author rmeier + * @version 05-12-2022 + */ +public class Msbnk2JSONLD { + private static final Logger logger = LogManager.getLogger(Msbnk2JSONLD.class); + + /** + * Validate a recordString and return the parsed information in a {@link Record} + * or null if the validation was not successful. Options are given in + * config. + */ + public static Record validate(String recordString, Set config) { + Record record = new Record(); + RecordParser recordparser = new RecordParser(record, config); + Result res = recordparser.parse(recordString); + if (res.isFailure()) { + logger.error(res.getMessage()); + int position = res.getPosition(); + String[] tokens = recordString.split("\\n"); + + int line = 0, col = 0, offset = 0; + for (String token : tokens) { + offset = offset + token.length() + 1; + if (position < offset) { + col = position - (offset - (token.length() + 1)); + logger.error(tokens[line]); + StringBuilder error_at = new StringBuilder(StringUtils.repeat(" ", col)); + error_at.append('^'); + logger.error(error_at); + break; + } + line++; + } + return null; + } + return record; + } + + public static void main(String[] arguments) { + // load version and print + final Properties properties = new Properties(); + try { + properties.load(ClassLoader.getSystemClassLoader().getResourceAsStream("project.properties")); + } catch (IOException e) { + e.printStackTrace(); + System.exit(1); + } + System.out.println("Msbnk2JSONLD version: " + properties.getProperty("version")); + + // parse command line + Options options = new Options(); + options.addRequiredOption("o", "out", true, "output file"); + CommandLine cmd = null; + try { + cmd = new DefaultParser().parse( options, arguments); + } + catch(ParseException e) { + // oops, something went wrong + System.err.println( "Parsing command line failed. Reason: " + e.getMessage() ); + HelpFormatter formatter = new HelpFormatter(); + formatter.printHelp("Validator [OPTIONS] [ ...]", options); + System.exit(1); + } + if (cmd.getArgList().size() == 0) { + HelpFormatter formatter = new HelpFormatter(); + formatter.printHelp("Validator [OPTIONS] [ ...]", options); + System.exit(1); + } + File outFile = new File(cmd.getOptionValue("o")); + System.out.println("Export to: " + outFile.toString()); + + // find all files in arguments and all *.txt files in directories and subdirectories + // specified in arguments + List recordfiles = new ArrayList<>(); + for (String argument : cmd.getArgList()) { + File argumentf = new File(argument); + if (argumentf.isFile() && FilenameUtils.getExtension(argument).equals("txt")) { + recordfiles.add(argumentf); + } + else if (argumentf.isDirectory()) { + recordfiles.addAll(FileUtils.listFiles(argumentf, new String[] {"txt"}, true)); + } + else { + logger.warn("Argument " + argument + " could not be processed."); + } + } + if (recordfiles.size() == 0 ) { + logger.error("No files found for validation."); + System.exit(1); + } + logger.trace("Found " + recordfiles.size() + " files"); + + // process all files + JsonArray structuredData = new JsonArray(); + recordfiles.parallelStream().map(filename -> { + Record record=null; + logger.info("Working on " + filename + "."); + try { + String recordString = FileUtils.readFileToString(filename, StandardCharsets.UTF_8); + Set config = new HashSet(); + config.add("legacy"); + record = validate(recordString, config); + if (record == null) { + logger.error("Error in \'" + filename + "\'."); + } + } catch (IOException e) { + e.printStackTrace(); + System.exit(1); + } + return record; + }) + .filter(Objects::nonNull) + .forEach(record -> { + structuredData.addAll(record.createStructuredDataJsonArray()); + }); + + //write results to file + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + try (BufferedWriter writer = new BufferedWriter(new FileWriter(outFile))) { + writer.write(gson.toJson(structuredData)); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } +} diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/RefreshDatabase.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/RefreshDatabase.java index c1adc4c1..b7c00cfb 100644 --- a/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/RefreshDatabase.java +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/cli/RefreshDatabase.java @@ -20,32 +20,22 @@ ******************************************************************************/ package massbank.cli; -import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; -import java.nio.charset.StandardCharsets; import java.sql.PreparedStatement; import java.sql.SQLException; -import java.util.ArrayList; -import java.util.HashSet; import java.util.List; -import java.util.Map; -import java.util.Objects; import java.util.Properties; -import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; -import java.util.stream.Collectors; -import java.util.stream.Stream; - import org.apache.commons.configuration2.ex.ConfigurationException; -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.filefilter.DirectoryFileFilter; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import massbank.Config; import massbank.Record; import massbank.db.DatabaseManager; +import massbank.repository.RepositoryInterface; +import massbank.repository.SimpleFileRepository; /** * This class is called from command line to create a new temporary @@ -53,7 +43,7 @@ * and move the new database to dbName. * * @author rmeier - * @version 10-06-2020 + * @version 24-01-2023 */ public class RefreshDatabase { private static final Logger logger = LogManager.getLogger(RefreshDatabase.class); @@ -69,61 +59,31 @@ public static void main(String[] args) throws FileNotFoundException, SQLExceptio } System.out.println("RefreshDatabase version: " + properties.getProperty("version")); - logger.trace("Creating a new database \""+ Config.get().tmpdbName() +"\" and initialize a MassBank database scheme."); + logger.info("Creating a new database \""+ Config.get().tmpdbName() +"\" and initialize a MassBank database scheme."); DatabaseManager.init_db(Config.get().tmpdbName()); logger.trace("Creating a DatabaseManager for \"" + Config.get().tmpdbName() + "\"."); final DatabaseManager db = new DatabaseManager(Config.get().tmpdbName()); - logger.trace("Get version of data source."); - String version = FileUtils.readFileToString(new File(Config.get().DataRootPath()+"/VERSION"), StandardCharsets.UTF_8); - - logger.info("Opening DataRootPath \"" + Config.get().DataRootPath() + "\" and iterate over content."); - File dataRootPath = new File(Config.get().DataRootPath()); - List recordfiles = new ArrayList<>(); - for (String file : dataRootPath.list(DirectoryFileFilter.INSTANCE)) { - if (file.equals(".scripts")) continue; - if (file.equals(".figure")) continue; - recordfiles.addAll(FileUtils.listFiles(new File(dataRootPath, file), new String[] {"txt"}, true)); - } - - AtomicInteger index = new AtomicInteger(0); - int chunkSize = 5000; - Stream> chunkedRecordfiles = recordfiles.stream().collect(Collectors.groupingBy(x -> index.getAndIncrement() / chunkSize)) - .entrySet().stream() - .map(Map.Entry::getValue); + RepositoryInterface repo = new SimpleFileRepository(); + List records = repo.getRecords(); - AtomicInteger processed = new AtomicInteger(1); - int numRecordFiles = recordfiles.size(); - chunkedRecordfiles.forEach(chunk -> { - chunk.parallelStream().map(filename -> { - Record record=null; - logger.info("Validating \"" + filename + "\"."); - String contributor = filename.getParentFile().getName(); - try { - String recordAsString = FileUtils.readFileToString(filename, StandardCharsets.UTF_8); - Set config = new HashSet(); - config.add("legacy"); - record = Validator.validate(recordAsString, config); - } catch (IOException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - if (record == null) { - logger.error("Error reading/validating record \"" + filename.toString() + "\"."); - } - return record; - }) - .filter(Objects::nonNull) - .forEachOrdered((r) -> { - db.persistAccessionFile(r); - System.out.print("Processed: "+processed.getAndIncrement()+"/"+numRecordFiles+"\r"); - }); + logger.info(records.size() + " records ready to be send to database."); + AtomicInteger currentIndex = new AtomicInteger(1); + int numRecordsOnePercent = records.size()/100+1; + System.out.print(records.size() + " records to send to database. 0% Done."); + records.stream().forEach((r) -> { + db.persistAccessionFile(r); + int index=currentIndex.getAndIncrement(); + if (index%numRecordsOnePercent == 0) { + System.out.print("\r" + records.size() + " records to send to database. " + 100*index/records.size() + "% Done."); + } }); + System.out.println("\r" + records.size() + " records to send to database. 100% Done"); - logger.trace("Setting Timestamp in database"); - PreparedStatement stmnt = db.getConnection().prepareStatement("INSERT INTO LAST_UPDATE (TIME,VERSION) VALUES (CURRENT_TIMESTAMP,?);"); - stmnt.setString(1, version); + logger.info("Setting version of database to: " + repo.getRepoVersion() + "."); + PreparedStatement stmnt = db.getConnection().prepareStatement("INSERT INTO LAST_UPDATE (LAST_UPDATE,VERSION) VALUES (CURRENT_TIMESTAMP,?);"); + stmnt.setString(1, repo.getRepoVersion()); stmnt.executeUpdate(); db.getConnection().commit(); db.closeConnection(); diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/db/DatabaseManager.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/db/DatabaseManager.java index 46140456..47008d6b 100755 --- a/MassBank-Project/MassBank-lib/src/main/java/massbank/db/DatabaseManager.java +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/db/DatabaseManager.java @@ -32,6 +32,7 @@ import java.sql.ResultSet; import java.sql.SQLException; import java.sql.Statement; +import java.sql.Timestamp; import java.util.ArrayList; import java.util.Arrays; import java.util.Iterator; @@ -112,9 +113,9 @@ public class DatabaseManager { private final static String selectINSTRUMENT = "SELECT * FROM INSTRUMENT WHERE ID = ?"; private final PreparedStatement statementSelectINSTRUMENT; // TABLE RECORD - private final static String insertRECORD = "INSERT INTO RECORD(ACCESSION, RECORD_TITLE, DATE, AUTHORS, LICENSE, COPYRIGHT, PUBLICATION," + + private final static String insertRECORD = "INSERT INTO RECORD(ACCESSION, RECORD_TIMESTAMP, RECORD_TITLE, DATE, AUTHORS, LICENSE, COPYRIGHT, PUBLICATION," + "CH, SP, AC_INSTRUMENT, AC_MASS_SPECTROMETRY_MS_TYPE, AC_MASS_SPECTROMETRY_ION_MODE, PK_SPLASH, CONTRIBUTOR)" + - "VALUES(?,?,?,?,?,?,?,?,?,?,?,?,?,?)"; + "VALUES(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)"; private final PreparedStatement statementInsertRECORD; private final static String selectRECORD = "SELECT * FROM RECORD WHERE ACCESSION = ?"; private final PreparedStatement statementSelectRECORD; @@ -523,37 +524,33 @@ public void persistAccessionFile(Record acc) { set.next(); int instrumentId = set.getInt("ID"); - //System.out.println(System.nanoTime()); statementInsertRECORD.setString(1, acc.ACCESSION()); - statementInsertRECORD.setString(2, acc.RECORD_TITLE1()); - statementInsertRECORD.setString(3, acc.DATE()); - statementInsertRECORD.setString(4, acc.AUTHORS()); - // if (acc.get("LICENSE").size() != 0) { - statementInsertRECORD.setString(5, acc.LICENSE()); - // } else { - // statementInsertRECORD.setNull(5, java.sql.Types.VARCHAR); - // } + statementInsertRECORD.setTimestamp(2, Timestamp.from(acc.getTimestamp())); + statementInsertRECORD.setString(3, acc.RECORD_TITLE1()); + statementInsertRECORD.setString(4, acc.DATE()); + statementInsertRECORD.setString(5, acc.AUTHORS()); + statementInsertRECORD.setString(6, acc.LICENSE()); if (acc.COPYRIGHT() != null) { - statementInsertRECORD.setString(6, acc.COPYRIGHT()); + statementInsertRECORD.setString(7, acc.COPYRIGHT()); } else { - statementInsertRECORD.setNull(6, java.sql.Types.VARCHAR); + statementInsertRECORD.setNull(7, java.sql.Types.VARCHAR); } if (acc.PUBLICATION() != null) { - statementInsertRECORD.setString(7, acc.PUBLICATION()); + statementInsertRECORD.setString(8, acc.PUBLICATION()); } else { - statementInsertRECORD.setNull(7, java.sql.Types.VARCHAR); + statementInsertRECORD.setNull(8, java.sql.Types.VARCHAR); } - statementInsertRECORD.setInt(8, compoundId); + statementInsertRECORD.setInt(9, compoundId); if (sampleId > 0) { - statementInsertRECORD.setInt(9, sampleId); + statementInsertRECORD.setInt(10, sampleId); } else { - statementInsertRECORD.setNull(9, java.sql.Types.INTEGER); + statementInsertRECORD.setNull(10, java.sql.Types.INTEGER); } - statementInsertRECORD.setInt(10, instrumentId); - statementInsertRECORD.setString(11, acc.AC_MASS_SPECTROMETRY_MS_TYPE()); - statementInsertRECORD.setString(12, acc.AC_MASS_SPECTROMETRY_ION_MODE()); - statementInsertRECORD.setString(13, acc.PK_SPLASH()); - statementInsertRECORD.setInt(14, contributorId); + statementInsertRECORD.setInt(11, instrumentId); + statementInsertRECORD.setString(12, acc.AC_MASS_SPECTROMETRY_MS_TYPE()); + statementInsertRECORD.setString(13, acc.AC_MASS_SPECTROMETRY_ION_MODE()); + statementInsertRECORD.setString(14, acc.PK_SPLASH()); + statementInsertRECORD.setInt(15, contributorId); statementInsertRECORD.executeUpdate(); //System.out.println(System.nanoTime()); @@ -757,6 +754,7 @@ public Record getAccessionData(String accessionId) { int instrumentID = -1; if (set.next()) { acc.ACCESSION(set.getString("ACCESSION")); + acc.setTimestamp(set.getTimestamp("RECORD_TIMESTAMP").toInstant()); acc.RECORD_TITLE1(set.getString("RECORD_TITLE")); acc.DATE(set.getString("DATE")); acc.AUTHORS(set.getString("AUTHORS")); diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/db/DatabaseTimestamp.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/db/DatabaseTimestamp.java index 906c7ea4..229cd71d 100644 --- a/MassBank-Project/MassBank-lib/src/main/java/massbank/db/DatabaseTimestamp.java +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/db/DatabaseTimestamp.java @@ -23,85 +23,92 @@ import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.Date; - +import java.time.Instant; import org.apache.commons.configuration2.ex.ConfigurationException; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; /** * - * DatabaseTimestamp checks COLUMN 'TIME' in TABLE 'LAST_UPDATE' in database - * 'MassBank' for the latest update time. DatabaseTimestamp is constructed with the - * current timestamp in the database and can be used to label external resources - * with a timestamp. {@code isOutdated()} is used to compare this timestamp to the - * current on in the database. + * DatabaseTimestamp retrieves COLUMN 'LAST_UPDATE' in TABLE 'LAST_UPDATE' from + * database 'MassBank' for the latest update time of the database. + * {@code isOutdated()} is used to compare this.timestamp with the latest state + * in the database. * * @author rmeier - * @version 23-08-2019 + * @version 01-02-2023 * */ public class DatabaseTimestamp { private static final Logger logger = LogManager.getLogger(DatabaseTimestamp.class); - private Date timestamp = new Date(); + private Instant timestamp = Instant.ofEpochSecond(0); private String version = "unknown"; - - public DatabaseTimestamp() throws SQLException, ConfigurationException { + + public DatabaseTimestamp() { // get timestamp of last db change from database - DatabaseManager databaseManager; - databaseManager = new DatabaseManager("MassBank"); - PreparedStatement stmnt = databaseManager.getConnection().prepareStatement("SELECT MAX(TIME) FROM LAST_UPDATE;"); - ResultSet res = stmnt.executeQuery(); - res.next(); - Date db_timestamp = res.getTimestamp(1); - if ( db_timestamp == null) { - logger.error("Timestamp from database is 'null'; using defaults."); - } - else { - timestamp = db_timestamp; - } - stmnt = databaseManager.getConnection().prepareStatement("SELECT MAX(VERSION) FROM LAST_UPDATE;"); - res = stmnt.executeQuery(); - res.next(); - String db_version = res.getString(1); - if ( db_version == null) { - logger.error("Version from database is 'null'; using defaults."); + try { + DatabaseManager databaseManager = new DatabaseManager("MassBank"); + PreparedStatement stmnt = databaseManager.getConnection() + .prepareStatement("SELECT MAX(LAST_UPDATE),VERSION FROM LAST_UPDATE;"); + ResultSet res = stmnt.executeQuery(); + res.next(); + Instant db_timestamp = res.getTimestamp(1).toInstant(); + String db_version = res.getString(2); + if (db_timestamp == null) { + logger.error("Timestamp from database is \"null\". Using defaults."); + } else { + timestamp = db_timestamp; + } + if (db_version == null) { + logger.error("Version from database is \"null\"."); + } else { + version = db_version; + } + databaseManager.closeConnection(); + logger.trace("Construct DatabaseTimestamp with timestamp \"" + timestamp + "\" and version \"" + db_version + + "\""); + } catch (SQLException | ConfigurationException e) { + logger.error("Error constructing DatabaseTimestamp from database value.", e);// TODO Auto-generated catch + // block } - else { - version = db_version; - } - - databaseManager.closeConnection(); - logger.trace("Create DatabaseTimestamp with: " + timestamp); + } - + /** - * Check if this timestamp is outdated. + * Check if this.timestamp is outdated. * - * @return Return true if the current database timestamp is more recent than this one. + * @return Return true if the current database timestamp is more recent than + * this.timestamp. * */ - public boolean isOutdated() throws SQLException, ConfigurationException { + public boolean isOutdated() { // check if this.timestamp is older than timestamp from database - DatabaseManager databaseManager; - databaseManager = new DatabaseManager("MassBank"); - PreparedStatement stmnt = databaseManager.getConnection().prepareStatement("SELECT MAX(TIME) FROM LAST_UPDATE"); - ResultSet res = stmnt.executeQuery(); - res.next(); - Date db_timestamp = res.getTimestamp(1); - if ( db_timestamp== null) { - db_timestamp = new Date(); - logger.error("Timestamp from database is 'null'; using defaults."); + try { + DatabaseManager databaseManager; + databaseManager = new DatabaseManager("MassBank"); + PreparedStatement stmnt = databaseManager.getConnection() + .prepareStatement("SELECT MAX(LAST_UPDATE) FROM LAST_UPDATE"); + ResultSet res = stmnt.executeQuery(); + res.next(); + Instant db_timestamp = res.getTimestamp(1).toInstant(); + if (db_timestamp == null) { + logger.error("Timestamp from database is \"null\". Return \"false\"."); + return false; + } + databaseManager.closeConnection(); + logger.trace("Found DatabaseTimestamp: " + db_timestamp); + logger.trace("Own Timestamp: " + timestamp); + logger.trace("isOutdated(): " + timestamp.isBefore(db_timestamp)); + return timestamp.isBefore(db_timestamp); + } catch (SQLException | ConfigurationException e) { + logger.error("Error retrieving timestamp from database. Return \"false\"", e); + return false; } - databaseManager.closeConnection(); - logger.trace("Found DatabaseTimestamp: " + db_timestamp); - logger.trace("Own Timestamp: " + timestamp); - logger.trace("isOutdated(): " + timestamp.before(db_timestamp)); - return timestamp.before(db_timestamp); } - + /** - * Return the String of the 'VERSION' file from the data repo at the time of database creation. + * Return the String of the 'VERSION' file from the data repo at the time of + * database creation. * * @return Return the version. * diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/repository/RepositoryInterface.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/repository/RepositoryInterface.java new file mode 100644 index 00000000..4880a6eb --- /dev/null +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/repository/RepositoryInterface.java @@ -0,0 +1,41 @@ +/******************************************************************************* + * Copyright (C) 2017 MassBank consortium + * + * This file is part of MassBank. + * + * MassBank is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + * + ******************************************************************************/ +package massbank.repository; + +import java.util.List; +import massbank.Record; + +/** + * Interface for a repository with some kind of data. + * @author rmeier + * @version 13-01-2023 + */ +public interface RepositoryInterface { + + /** + * Return all Records of that repo in a stream. + */ + public List getRecords(); + /** + * Return a version String for the repo. + */ + public String getRepoVersion(); +} diff --git a/MassBank-Project/MassBank-lib/src/main/java/massbank/repository/SimpleFileRepository.java b/MassBank-Project/MassBank-lib/src/main/java/massbank/repository/SimpleFileRepository.java new file mode 100644 index 00000000..0a55abae --- /dev/null +++ b/MassBank-Project/MassBank-lib/src/main/java/massbank/repository/SimpleFileRepository.java @@ -0,0 +1,118 @@ +/******************************************************************************* + * Copyright (C) 2017 MassBank consortium + * + * This file is part of MassBank. + * + * MassBank is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + * + ******************************************************************************/ +package massbank.repository; + +import java.io.File; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.time.Instant; +import java.time.ZonedDateTime; +import java.time.format.DateTimeFormatter; +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; +import java.util.Set; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Collectors; +import org.apache.commons.configuration2.Configuration; +import org.apache.commons.configuration2.builder.fluent.Configurations; +import org.apache.commons.configuration2.ex.ConfigurationException; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.filefilter.DirectoryFileFilter; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; + +import massbank.Config; +import massbank.Record; +import massbank.cli.Validator; + +/** + * This class implements a classical MassBank repository with record files + * in directories, but no subdirectories as in MassBank-data. It reads a + * file named 'VERSION' with a version String for the whole repo and a + * timestamp, which is applied to all Records. + * @author rmeier + * @version 13-01-2023 + */ +public class SimpleFileRepository implements RepositoryInterface { + private static final Logger logger = LogManager.getLogger(SimpleFileRepository.class); + private String version; + List records; + + public SimpleFileRepository() throws ConfigurationException { + logger.info("Opening DataRootPath \"" + Config.get().DataRootPath() + "\" and iterate over content."); + File dataRootPath = new File(Config.get().DataRootPath()); + // get version and timestamp + Configurations configs = new Configurations(); + Configuration versionconfig = configs.properties(new File(dataRootPath, "VERSION")); + + version = versionconfig.getString("version"); + logger.info("Repo version: " + version); + + Instant timestamp = ZonedDateTime.parse(versionconfig.getString("timestamp"), DateTimeFormatter.ISO_OFFSET_DATE_TIME).toInstant(); + logger.info("Repo timestamp: " + timestamp); + + List recordfiles = new ArrayList<>(); + for (String file : dataRootPath.list(DirectoryFileFilter.INSTANCE)) { + if (file.startsWith(".")) continue; + recordfiles.addAll(FileUtils.listFiles(new File(dataRootPath, file), new String[] {"txt"}, false)); + } + logger.info("Found " + recordfiles.size() + " records in repo."); + + AtomicInteger currentIndex = new AtomicInteger(1); + int numRecordFilesOnePercent = recordfiles.size()/100+1; + System.out.print(recordfiles.size() + " records to read. 0% Done."); + + records = recordfiles.parallelStream().map(filename -> { + Record record = null; + logger.trace("Working on \'" + filename + "\'."); + try { + String recordString = FileUtils.readFileToString(filename, StandardCharsets.UTF_8); + record = Validator.validate(recordString, Set.of("legacy")); + if (record == null) { + logger.error("Error in \'" + filename + "\'."); + } + else { + record.setTimestamp(timestamp); + } + } catch (IOException e) { + logger.error("Error reading record \"" + filename.toString() + "\". File will be ignored.\n", e); + } + int index=currentIndex.getAndIncrement(); + if (index%numRecordFilesOnePercent == 0) { + System.out.print("\r" + recordfiles.size() + " records to read. " + 100*index/recordfiles.size() + "% Done."); + } + return record; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()); + System.out.println("\r" + recordfiles.size() + " records to read. 100% Done."); + logger.info("Successfully read " + records.size() + " records in repo."); + } + + public List getRecords() { + return records; + } + + public String getRepoVersion() { + return version; + } +} diff --git a/MassBank-Project/MassBank-lib/src/main/resources-filtered/project.properties b/MassBank-Project/MassBank-lib/src/main/resources-filtered/project.properties index e5683df8..13c2d766 100644 --- a/MassBank-Project/MassBank-lib/src/main/resources-filtered/project.properties +++ b/MassBank-Project/MassBank-lib/src/main/resources-filtered/project.properties @@ -1 +1,2 @@ -version=${project.version} \ No newline at end of file +version=${project.version} +timestamp=${timestamp} \ No newline at end of file diff --git a/MassBank-Project/MassBank-lib/src/main/resources/create_massbank_scheme.sql b/MassBank-Project/MassBank-lib/src/main/resources/create_massbank_scheme.sql index 910d34cd..b457e321 100644 --- a/MassBank-Project/MassBank-lib/src/main/resources/create_massbank_scheme.sql +++ b/MassBank-Project/MassBank-lib/src/main/resources/create_massbank_scheme.sql @@ -90,6 +90,7 @@ CREATE TABLE INSTRUMENT ( CREATE TABLE RECORD ( ACCESSION VARCHAR(255) NOT NULL UNIQUE, + RECORD_TIMESTAMP TIMESTAMP, RECORD_TITLE VARCHAR(600) NOT NULL, DATE VARCHAR(600) NOT NULL, AUTHORS VARCHAR(600) NOT NULL, @@ -246,7 +247,7 @@ CREATE TABLE ANNOTATION ( ); CREATE TABLE LAST_UPDATE ( - TIME TIMESTAMP, + LAST_UPDATE TIMESTAMP, VERSION VARCHAR(100) ); diff --git a/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.obo b/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.obo new file mode 100644 index 00000000..13423d5a --- /dev/null +++ b/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.obo @@ -0,0 +1,23279 @@ +format-version: 1.2 +data-version: 4.1.103 +date: 21:09:2022 11:38 +saved-by: Joshua Klein +auto-generated-by: OBO-Edit 2.3.1 +import: http://purl.obolibrary.org/obo/pato.obo +import: http://purl.obolibrary.org/obo/stato.owl +default-namespace: MS +namespace-id-rule: * MS:$sequence(7,0,9999999)$ +namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ +remark: coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics +remark: namespace: MS +remark: namespace: PEFF +remark: coverage: Mass spectrometer output files and spectra interpretation +remark: creator: Yasset Perez-Riverol ebi.ac.uk> +remark: creator: Matt Chambers vanderbilt.edu> +remark: creator: Andreas Bertsch informatik.uni-tuebingen.de> +remark: creator: Marius Kallhardt bdal.de> +remark: creator: Eric Deutsch systemsbiology.org> +remark: creator: Fredrik Levander immun.lth.se> +remark: creator: Pierre-Alain Binz chuv.ch> +remark: creator: Gerhard Mayer rub.de> +remark: creator: Joshua Klein bu.edu> +remark: creator: Chris Bielow fu-berlin.de> +remark: creator: Wout Bittremieux health.ucsd.edu> +remark: creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de> +remark: creator: Julian Uszkoreit ruhr-uni-bochum.de> +remark: creator: Mathias Walzer ebi.ac.uk> +remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group +remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page +remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net +remark: URL: http://purl.obolibrary.org/obo/ms/psi-ms.obo +remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. +remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. +ontology: ms + +[Typedef] +id: has_regexp +name: has regexp + +[Typedef] +id: has_units +name: has_units + +[Typedef] +id: part_of +name: part_of +is_transitive: true + +[Typedef] +id: has_order +name: has_order + +[Typedef] +id: has_domain +name: has_domain + +[Typedef] +id: has_value_type +name: has value type +def: "'Entity A' has value type 'Entity B', such as xsd:float." [] + +[Typedef] +id: has_structured_representation_in_format +name: has structured representation in format +def: "The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format." [] + +[Typedef] +id: has_metric_category +name: has_metric_category + +[Typedef] +id: has_value_concept +name: has_value_concept + +[Typedef] +id: has_column +name: has_column + +[Typedef] +id: has_optional_column +name: has_optional_column + +[Term] +id: NCIT:C25330 +name: Duration +def: "The period of time during which something continues." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C21514 ! Temporal Qualifier + +[Term] +id: NCIT:C45781 +name: Density +def: "The amount of something per unit size." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C25447 ! Characteristic + +[Term] +id: NCIT:C68811 +name: Cover +def: "Span a region or interval of distance, space or time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C25404 ! Action + +[Term] +id: NCIT:C79083 +name: Outlier +def: "An observation in a data set that is numerically distant from the rest of the data." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C20181 ! Conceptual Entity + +[Term] +id: NCIT:C21514 +name: Temporal Qualifier +def: "Terms used to indicate units of time or other terms associated with time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} +is_a: NCIT:C41009 ! Qualifier + +[Term] +id: NCIT:C41009 +name: Qualifier +def: "A term that helps define and render a concept unique." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Modifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +is_a: NCIT:C20189 ! Property or Attribute + +[Term] +id: NCIT:C25447 +name: Characteristic +def: "The distinguishing qualities or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} +synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} +synonym: "Characteristics" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Feature" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Features" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} +is_a: NCIT:C20189 ! Property or Attribute + +[Term] +id: NCIT:C20189 +name: Property or Attribute +def: "A distinguishing quality or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} + +[Term] +id: NCIT:C25404 +name: Action +def: "A thing done." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +subset: NCIT:C105763 +synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} +synonym: "Generic Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +is_a: NCIT:C43431 ! Activity + +[Term] +id: NCIT:C43431 +name: Activity +def: "An active process; excludes processes and mechanisms which fulfill biological functions." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} +synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 3.0.3"} +synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 5.3"} +synonym: "General activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} + +[Term] +id: NCIT:C20181 +name: Conceptual Entity +def: "An organizational header for concepts representing mostly abstract entities." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Conceptual Entity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} + +[Term] +id: NCIT:C16847 +name: Technique +def: "A practiced and regimented skill or series of actions." [] {http://purl.obolibrary.org/obo/NCIT_C16847="NCI"} +is_a: NCIT:C43431 ! Activity + +[Term] +id: NCIT:C19044 +name: Statistical Technique +def: "A method of analyzing or representing statistical data; a procedure for calculating a statistic." [] {http://purl.obolibrary.org/obo/NCIT_C19044="NCI"} +is_a: NCIT:C16847 ! Technique + +[Term] +id: NCIT:C60694 +name: Principal Component +def: "One of the axes representing the projection of varience resulting from principal component analysis." [] {http://purl.obolibrary.org/obo/NCIT_C60694="NCI"} +is_a: NCIT:C19044 ! Statistical Technique + +[Term] +id: MS:0000000 +name: Proteomics Standards Initiative Mass Spectrometry Vocabularies +def: "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [PSI:MS] + +[Term] +id: MS:1000001 +name: sample number +def: "A reference number relevant to the sample under study." [PSI:MS] +is_a: MS:1000548 ! sample attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000002 +name: sample name +def: "A reference string relevant to the sample under study." [PSI:MS] +is_a: MS:1000548 ! sample attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000003 +name: sample state +def: "The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS] +is_a: MS:1000548 ! sample attribute + +[Term] +id: MS:1000004 +name: sample mass +def: "Total mass of sample used." [PSI:MS] +is_a: MS:1000548 ! sample attribute +relationship: has_units UO:0000021 ! gram +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000005 +name: sample volume +def: "Total volume of solution used." [PSI:MS] +is_a: MS:1000548 ! sample attribute +relationship: has_units UO:0000098 ! milliliter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000006 +name: sample concentration +def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] +is_a: MS:1000548 ! sample attribute +relationship: has_units UO:0000175 ! gram per liter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000007 +name: inlet type +def: "The nature of the sample inlet." [PSI:MS] +relationship: part_of MS:1000458 ! source + +[Term] +id: MS:1000008 +name: ionization type +def: "The method by which gas phase ions are generated from the sample." [PSI:MS] +relationship: part_of MS:1000458 ! source + +[Term] +id: MS:1000009 +name: ionization mode +def: "OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer." [PSI:MS] +comment: This term was made obsolete because it was replaced by scan polarity (MS:1000465). +is_obsolete: true + +[Term] +id: MS:1000010 +name: analyzer type +def: "OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000011 +name: mass resolution +def: "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000012 +name: resolution measurement method +def: "Which of the available standard measures is used to define whether two peaks are separate." [PSI:MS] +is_a: MS:1000596 ! measurement method + +[Term] +id: MS:1000013 +name: resolution type +def: "OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000014 +name: accuracy +def: "Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS] +is_a: MS:1000480 ! mass analyzer attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000015 +name: scan rate +def: "Rate in Th/sec for scanning analyzers." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_units MS:1000807 ! Th/s +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000016 +name: scan start time +def: "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS] +is_a: MS:1000503 ! scan attribute +is_a: MS:1002345 ! PSM-level attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000017 +name: Scan Function +def: "OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum." [PSI:MS] +comment: OBSOLETE This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000018 +name: scan direction +def: "Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low)." [PSI:MS] +relationship: part_of MS:1000441 ! scan + +[Term] +id: MS:1000019 +name: scan law +def: "Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used." [PSI:MS] +relationship: part_of MS:1000441 ! scan + +[Term] +id: MS:1000020 +name: scanning method +def: "Describes the acquisition data type produced by a tandem mass spectrometry experiment." [PSI:MS] +comment: OBSOLETE This former purgatory term was made obsolete. +synonym: "Tandem Scanning Method" RELATED [] +is_obsolete: true + +[Term] +id: MS:1000021 +name: reflectron state +def: "Status of the reflectron, turned on or off." [PSI:MS] +is_a: MS:1000480 ! mass analyzer attribute + +[Term] +id: MS:1000022 +name: TOF Total Path Length +def: "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000480 ! mass analyzer attribute +relationship: has_units UO:0000008 ! meter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000023 +name: isolation width +def: "OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS] +comment: This former purgatory term was made obsolete. +relationship: has_units MS:1000040 ! m/z +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000024 +name: final MS exponent +def: "Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS] +is_a: MS:1000480 ! mass analyzer attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1000025 +name: magnetic field strength +def: "A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity." [PSI:MS] +synonym: "B" EXACT [] +synonym: "Magnetic Field" RELATED [] +is_a: MS:1000480 ! mass analyzer attribute +relationship: has_units UO:0000228 ! tesla +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000026 +name: detector type +def: "Type of detector used in the mass spectrometer." [PSI:MS] +relationship: part_of MS:1000453 ! detector + +[Term] +id: MS:1000027 +name: detector acquisition mode +def: "Method by which detector signal is acquired by the data system." [PSI:MS] +relationship: part_of MS:1000453 ! detector + +[Term] +id: MS:1000028 +name: detector resolution +def: "The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height." [PSI:MS] +is_a: MS:1000481 ! detector attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000029 +name: sampling frequency +def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS] +synonym: "ADC Sampling Frequency" NARROW [] +is_a: MS:1000481 ! detector attribute +relationship: has_units UO:0000106 ! hertz +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000030 +name: vendor +def: "OBSOLETE Name of instrument vendor." [PSI:MS] +comment: This term was made obsolete because it was replaced by instrument model (MS:1000031). +is_obsolete: true + +[Term] +id: MS:1000031 +name: instrument model +def: "Instrument model name not including the vendor's name." [PSI:MS] +relationship: part_of MS:1000463 ! instrument + +[Term] +id: MS:1000032 +name: customization +def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS] +is_a: MS:1000496 ! instrument attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000033 +name: deisotoping +def: "The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1000034 +name: charge deconvolution +def: "The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1000035 +name: peak picking +def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1000036 +name: scan mode +def: "OBSOLETE." [PSI:MS] +comment: This term was made obsolete because . +is_obsolete: true + +[Term] +id: MS:1000037 +name: polarity +def: "OBSOLETE Terms to describe the polarity setting of the instrument." [PSI:MS] +comment: This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186). +is_obsolete: true + +[Term] +id: MS:1000038 +name: minute +def: "OBSOLETE Acquisition time in minutes." [PSI:MS] +comment: This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031). +is_obsolete: true + +[Term] +id: MS:1000039 +name: second +def: "OBSOLETE Acquisition time in seconds." [PSI:MS] +comment: This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010). +is_obsolete: true + +[Term] +id: MS:1000040 +name: m/z +def: "Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated." [PSI:MS] +synonym: "mass-to-charge ratio" EXACT [] +synonym: "Th" EXACT [] +synonym: "thomson" EXACT [] +is_a: UO:0000000 ! unit + +[Term] +id: MS:1000041 +name: charge state +def: "Number of net charges, positive or negative, on an ion." [PSI:MS] +synonym: "z" EXACT [] +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1000507 ! ion property +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1000042 +name: peak intensity +def: "Intensity of ions as measured by the height or area of a peak in a mass spectrum." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 +relationship: has_units UO:0000269 ! absorbance unit +relationship: part_of MS:1000231 ! peak +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000043 +name: intensity unit +def: "Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors." [PSI:MS] +is_a: UO:0000000 ! unit + +[Term] +id: MS:1000044 +name: dissociation method +def: "Fragmentation method used for dissociation or fragmentation." [PSI:MS] +synonym: "Activation Method" RELATED [] +relationship: part_of MS:1000456 ! precursor activation + +[Term] +id: MS:1000045 +name: collision energy +def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000046 +name: energy unit +def: "OBSOLETE Energy units are represented in either eV or Joules." [PSI:MS] +comment: This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111). +is_a: UO:0000000 ! unit +is_obsolete: true + +[Term] +id: MS:1000047 +name: emulsion +def: "State if the sample is in emulsion form." [PSI:MS] +is_a: MS:1000003 ! sample state + +[Term] +id: MS:1000048 +name: gaseous sample state +def: "State if the sample is in gaseous form." [PSI:MS] +is_a: MS:1000003 ! sample state + +[Term] +id: MS:1000049 +name: liquid sample state +def: "State if the sample is in liquid form." [PSI:MS] +is_a: MS:1000003 ! sample state + +[Term] +id: MS:1000050 +name: solid sample state +def: "State if the sample is in solid form." [PSI:MS] +is_a: MS:1000003 ! sample state + +[Term] +id: MS:1000051 +name: solution +def: "State if the sample is in solution form." [PSI:MS] +is_a: MS:1000003 ! sample state + +[Term] +id: MS:1000052 +name: suspension +def: "State if the sample is in suspension form." [PSI:MS] +is_a: MS:1000003 ! sample state + +[Term] +id: MS:1000053 +name: sample batch +def: "Sample batch lot identifier." [PSI:MS] +is_a: MS:1000548 ! sample attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000054 +name: chromatography +def: "OBSOLETE Chromatographic conditions used to obtain the sample." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000055 +name: continuous flow fast atom bombardment +def: "Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix." [PSI:MS] +synonym: "CF-FAB" EXACT [] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000056 +name: direct inlet +def: "The sample is directly inserted into the ion source, usually on the end of a heatable probe." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000057 +name: electrospray inlet +def: "Inlet used for introducing the liquid sample into an electrospray ionization source." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000058 +name: flow injection analysis +def: "Sample is directly injected or infused into the ionization source." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000059 +name: inductively coupled plasma +def: "A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000060 +name: infusion +def: "The continuous flow of solution of a sample into the ionization source." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000061 +name: jet separator +def: "A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000062 +name: membrane separator +def: "A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000063 +name: moving belt +def: "Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000064 +name: moving wire +def: "Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000065 +name: open split +def: "A division of flowing stream of liquid into two streams." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000066 +name: particle beam +def: "Method for generating ions from a solution of an analyte." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000067 +name: reservoir +def: "A sample inlet method involving a reservoir." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000068 +name: septum +def: "A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000069 +name: thermospray inlet +def: "A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000070 +name: atmospheric pressure chemical ionization +def: "Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization." [PSI:MS] +synonym: "APCI" EXACT [] +is_a: MS:1000240 ! atmospheric pressure ionization + +[Term] +id: MS:1000071 +name: chemical ionization +def: "The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization." [PSI:MS] +synonym: "CI" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000072 +name: Electronic Ionization +def: "OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS] +comment: This term was made obsolete because it was replaced by electron ionization (MS:1000389). +synonym: "EI" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000073 +name: electrospray ionization +def: "A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended." [PSI:MS] +synonym: "ESI" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000074 +name: fast atom bombardment ionization +def: "The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization." [PSI:MS] +synonym: "FAB" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000075 +name: matrix-assisted laser desorption ionization +def: "The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization." [PSI:MS] +synonym: "MALDI" EXACT [] +is_a: MS:1000247 ! desorption ionization + +[Term] +id: MS:1000076 +name: negative ion mode +def: "OBSOLETE." [PSI:MS] +comment: This term was made obsolete because it was replaced by negative scan (MS:1000129). +is_obsolete: true + +[Term] +id: MS:1000077 +name: positive ion mode +def: "OBSOLETE." [PSI:MS] +comment: This term was made obsolete because it was replaced by positive scan (MS:1000130). +is_obsolete: true + +[Term] +id: MS:1000078 +name: axial ejection linear ion trap +def: "A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer." [PSI:MS] +is_a: MS:1000291 ! linear ion trap + +[Term] +id: MS:1000079 +name: fourier transform ion cyclotron resonance mass spectrometer +def: "A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z." [PSI:MS] +synonym: "FT_ICR" EXACT [] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000080 +name: magnetic sector +def: "A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z." [PSI:MS] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000081 +name: quadrupole +def: "A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000082 +name: quadrupole ion trap +def: "Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials." [PSI:MS] +synonym: "Paul Ion trap" EXACT [] +synonym: "QIT" EXACT [] +synonym: "Quistor" EXACT [] +is_a: MS:1000264 ! ion trap + +[Term] +id: MS:1000083 +name: radial ejection linear ion trap +def: "A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer." [PSI:MS] +is_a: MS:1000291 ! linear ion trap + +[Term] +id: MS:1000084 +name: time-of-flight +def: "Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy." [PSI:MS] +synonym: "TOF" EXACT [] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000085 +name: baseline +def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS] +is_a: MS:1000012 ! resolution measurement method + +[Term] +id: MS:1000086 +name: full width at half-maximum +def: "A measure of resolution represented as width of the peak at half peak height." [PSI:MS] +synonym: "FWHM" EXACT [] +is_a: MS:1000012 ! resolution measurement method + +[Term] +id: MS:1000087 +name: ten percent valley +def: "An attribute of resolution when the ratio between adjacent signals is 10% of the signal height." [PSI:MS] +is_a: MS:1000012 ! resolution measurement method + +[Term] +id: MS:1000088 +name: constant +def: "OBSOLETE When resolution is constant with respect to m/z." [PSI:MS] +comment: This child of the former purgatory term resolution type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000089 +name: proportional +def: "OBSOLETE When resolution is proportional with respect to m/z." [PSI:MS] +comment: This child of the former purgatory term resolution type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000090 +name: mass scan +def: "OBSOLETE A variation of instrument where a selected mass is scanned." [PSI:MS] +comment: This child of the former purgatory term Scan Function was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000091 +name: selected ion detection +def: "OBSOLETE Please see Single Ion Monitoring." [PSI:MS] +comment: This child of the former purgatory term Scan Function was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000092 +name: decreasing m/z scan +def: "High to low direction in terms of m/z of the scan for scanning analyzers." [PSI:MS] +is_a: MS:1000018 ! scan direction + +[Term] +id: MS:1000093 +name: increasing m/z scan +def: "Low to high direction in terms of m/z of the scan for scanning analyzers." [PSI:MS] +is_a: MS:1000018 ! scan direction + +[Term] +id: MS:1000094 +name: exponential +def: "The mass scan is done in exponential mode." [PSI:MS] +is_a: MS:1000019 ! scan law + +[Term] +id: MS:1000095 +name: linear +def: "OBSOLETE The mass scan is done in linear mode." [PSI:MS] +comment: This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199). +is_a: MS:1000019 ! scan law +is_obsolete: true + +[Term] +id: MS:1000096 +name: quadratic +def: "The mass scan is done in quadratic mode." [PSI:MS] +is_a: MS:1000019 ! scan law + +[Term] +id: MS:1000097 +name: constant neutral mass loss +def: "OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000098 +name: multiple ion monitoring +def: "OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000099 +name: multiple reaction monitoring +def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS] +comment: This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206). +synonym: "MRM" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000100 +name: precursor ion scan +def: "OBSOLETE The specific scan function or process that will record a precursor ion spectrum." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000101 +name: product ion scan +def: "OBSOLETE The specific scan function or process that records product ion spectrum." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000102 +name: single ion monitoring +def: "OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum." [PSI:MS] +comment: This term was made obsolete because it was replaced by single ion monitoring (MS:100205). +is_obsolete: true + +[Term] +id: MS:1000103 +name: single reaction monitoring +def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS] +comment: This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206). +is_obsolete: true + +[Term] +id: MS:1000104 +name: None ?? +def: "OBSOLETE None." [PSI:MS] +comment: This term was made obsolete because . +is_obsolete: true + +[Term] +id: MS:1000105 +name: reflectron off +def: "Reflectron is off." [PSI:MS] +is_a: MS:1000021 ! reflectron state + +[Term] +id: MS:1000106 +name: reflectron on +def: "Reflectron is on." [PSI:MS] +is_a: MS:1000021 ! reflectron state + +[Term] +id: MS:1000107 +name: channeltron +def: "A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse." [PSI:MS] +synonym: "Channeltron Detector" EXACT [] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000108 +name: conversion dynode electron multiplier +def: "A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] +is_a: MS:1000346 ! conversion dynode + +[Term] +id: MS:1000109 +name: conversion dynode photomultiplier +def: "A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier." [PSI:MS] +synonym: "ion-to-photon detector" RELATED [] +is_a: MS:1000346 ! conversion dynode + +[Term] +id: MS:1000110 +name: daly detector +def: "Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector." [PSI:MS] +synonym: "Daly" EXACT [] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000111 +name: electron multiplier tube +def: "A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons." [PSI:MS] +synonym: "EMT" EXACT [] +is_a: MS:1000253 ! electron multiplier + +[Term] +id: MS:1000112 +name: faraday cup +def: "A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000113 +name: focal plane array +def: "An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS] +is_a: MS:1000348 ! focal plane collector + +[Term] +id: MS:1000114 +name: microchannel plate detector +def: "A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate." [PSI:MS] +synonym: "multichannel plate" EXACT [] +is_a: MS:1000345 ! array detector + +[Term] +id: MS:1000115 +name: multi-collector +def: "A detector system commonly used in inductively coupled plasma mass spectrometers." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000116 +name: photomultiplier +def: "A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected." [PSI:MS] +synonym: "PMT" EXACT [] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000117 +name: analog-digital converter +def: "Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers." [PSI:MS] +synonym: "ADC" EXACT [] +is_a: MS:1000027 ! detector acquisition mode + +[Term] +id: MS:1000118 +name: pulse counting +def: "Definition to do." [PSI:MS] +is_a: MS:1000027 ! detector acquisition mode + +[Term] +id: MS:1000119 +name: time-digital converter +def: "A device for converting a signal of sporadic pluses into a digital representation of their time indices." [PSI:MS] +synonym: "TDC" EXACT [] +is_a: MS:1000027 ! detector acquisition mode + +[Term] +id: MS:1000120 +name: transient recorder +def: "A detector acquisition mode used for detecting transient signals." [PSI:MS] +is_a: MS:1000027 ! detector acquisition mode + +[Term] +id: MS:1000121 +name: SCIEX instrument model +def: "The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as \"Applied Biosystems|MDS SCIEX\"." [PSI:MS] +synonym: "Applied Biosystems|MDS SCIEX" RELATED [] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000122 +name: Bruker Daltonics instrument model +def: "Bruker Daltonics' instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000123 +name: IonSpec instrument model +def: "IonSpec corporation instrument model." [PSI:MS] +is_a: MS:1000489 ! Varian instrument model + +[Term] +id: MS:1000124 +name: Shimadzu instrument model +def: "Shimadzu corporation instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000125 +name: Thermo Finnigan instrument model +def: "ThermoFinnigan from Thermo Electron Corporation instrument model." [PSI:MS] +is_a: MS:1000483 ! Thermo Fisher Scientific instrument model + +[Term] +id: MS:1000126 +name: Waters instrument model +def: "Waters Corporation instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000127 +name: centroid spectrum +def: "Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset." [PSI:MS] +synonym: "Discrete Mass Spectrum" EXACT [] +is_a: MS:1000525 ! spectrum representation + +[Term] +id: MS:1000128 +name: profile spectrum +def: "A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis." [PSI:MS] +synonym: "continuous mass spectrum" EXACT [] +synonym: "Continuum Mass Spectrum" EXACT [] +is_a: MS:1000525 ! spectrum representation + +[Term] +id: MS:1000129 +name: negative scan +def: "Polarity of the scan is negative." [PSI:MS] +is_a: MS:1000465 ! scan polarity +is_a: MS:1000808 ! chromatogram attribute + +[Term] +id: MS:1000130 +name: positive scan +def: "Polarity of the scan is positive." [PSI:MS] +is_a: MS:1000465 ! scan polarity +is_a: MS:1000808 ! chromatogram attribute + +[Term] +id: MS:1000131 +name: number of detector counts +def: "The number of counted events observed in one or a group of elements of a detector." [PSI:MS] +is_a: MS:1000043 ! intensity unit + +[Term] +id: MS:1000132 +name: percent of base peak +def: "The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS] +is_a: MS:1000043 ! intensity unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000133 +name: collision-induced dissociation +def: "The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended." [PSI:MS] +synonym: "CID" EXACT [] +synonym: "CAD" EXACT [] +synonym: "collisionally activated dissociation" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000134 +name: plasma desorption +def: "The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization." [PSI:MS] +synonym: "PD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000135 +name: post-source decay +def: "A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra." [PSI:MS] +synonym: "PSD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000136 +name: surface-induced dissociation +def: "Fragmentation that results from the collision of an ion with a surface." [PSI:MS] +synonym: "SID" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000137 +name: electron volt +def: "OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J." [PSI:MS] +comment: This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266). +is_obsolete: true + +[Term] +id: MS:1000138 +name: normalized collision energy +def: "Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000139 +name: 4000 QTRAP +def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000140 +name: 4700 Proteomics Analyzer +def: "Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS." [PSI:MS] +is_a: MS:1000495 ! Applied Biosystems instrument model + +[Term] +id: MS:1000141 +name: apex IV +def: "Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] +is_a: MS:1001556 ! Bruker Daltonics apex series + +[Term] +id: MS:1000142 +name: apex Q +def: "Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] +is_a: MS:1001556 ! Bruker Daltonics apex series + +[Term] +id: MS:1000143 +name: API 150EX +def: "Applied Biosystems/MDS SCIEX API 150EX MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000144 +name: API 150EX Prep +def: "Applied Biosystems/MDS SCIEX API 150EX Prep MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000145 +name: API 2000 +def: "Applied Biosystems/MDS SCIEX API 2000 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000146 +name: API 3000 +def: "Applied Biosystems/MDS SCIEX API 3000 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000147 +name: API 4000 +def: "Applied Biosystems/MDS SCIEX API 4000 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000148 +name: autoflex II +def: "Bruker Daltonics' autoflex II: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000149 +name: autoflex TOF/TOF +def: "Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000150 +name: Auto Spec Ultima NT +def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000151 +name: BioTOF II +def: "Bruker Daltonics' BioTOF II: ESI TOF." [PSI:MS] +is_a: MS:1001535 ! Bruker Daltonics BioTOF series + +[Term] +id: MS:1000152 +name: BioTOF-Q +def: "Bruker Daltonics' BioTOF-Q: ESI Q-TOF." [PSI:MS] +is_a: MS:1001535 ! Bruker Daltonics BioTOF series + +[Term] +id: MS:1000153 +name: DELTA plusAdvantage +def: "ThermoFinnigan DELTA plusAdvantage MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000154 +name: DELTAplusXP +def: "ThermoFinnigan DELTAplusXP MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000155 +name: ELEMENT2 +def: "OBSOLETE ThermoFinnigan ELEMENT2 MS." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000156 +name: esquire 4000 +def: "Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1001533 ! Bruker Daltonics esquire series + +[Term] +id: MS:1000157 +name: esquire 6000 +def: "Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1001533 ! Bruker Daltonics esquire series + +[Term] +id: MS:1000158 +name: explorer +def: "IonSpec Explorer MS." [PSI:MS] +is_a: MS:1000123 ! IonSpec instrument model + +[Term] +id: MS:1000159 +name: GCT +def: "Waters oa-ToF based GCT." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000160 +name: HCT +def: "Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1000697 ! Bruker Daltonics HCT Series + +[Term] +id: MS:1000161 +name: HCTplus +def: "Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1000697 ! Bruker Daltonics HCT Series + +[Term] +id: MS:1000162 +name: HiRes ESI +def: "IonSpec HiResESI MS." [PSI:MS] +is_a: MS:1000123 ! IonSpec instrument model + +[Term] +id: MS:1000163 +name: HiRes MALDI +def: "IonSpec HiResMALDI MS." [PSI:MS] +is_a: MS:1000123 ! IonSpec instrument model + +[Term] +id: MS:1000164 +name: IsoPrime +def: "Waters IsoPrime MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000165 +name: IsoProbe +def: "Waters IsoProbe MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000166 +name: IsoProbe T +def: "Waters IsoProbe T MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000167 +name: LCQ Advantage +def: "ThermoFinnigan LCQ Advantage MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000168 +name: LCQ Classic +def: "ThermoFinnigan LCQ Classic MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000169 +name: LCQ Deca XP Plus +def: "ThermoFinnigan LCQ Deca XP Plus MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000170 +name: M@LDI L +def: "Waters oa-ToF based MALDI L." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000171 +name: M@LDI LR +def: "Waters oa-ToF based MALDI LR." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000172 +name: MAT253 +def: "ThermoFinnigan MAT253 MS." [PSI:MS] +is_a: MS:1000493 ! Finnigan MAT instrument model + +[Term] +id: MS:1000173 +name: MAT900XP +def: "ThermoFinnigan MAT900XP MS." [PSI:MS] +is_a: MS:1000493 ! Finnigan MAT instrument model + +[Term] +id: MS:1000174 +name: MAT900XP Trap +def: "ThermoFinnigan MAT900XP Trap MS." [PSI:MS] +is_a: MS:1000493 ! Finnigan MAT instrument model + +[Term] +id: MS:1000175 +name: MAT95XP +def: "ThermoFinnigan MAT95XP MS." [PSI:MS] +is_a: MS:1000493 ! Finnigan MAT instrument model + +[Term] +id: MS:1000176 +name: MAT95XP Trap +def: "ThermoFinnigan MAT95XP Trap MS." [PSI:MS] +is_a: MS:1000493 ! Finnigan MAT instrument model + +[Term] +id: MS:1000177 +name: microflex +def: "Bruker Daltonics' microflex: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000178 +name: microTOF LC +def: "Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1000179 +name: neptune +def: "ThermoFinnigan NEPTUNE MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000180 +name: NG-5400 +def: "Waters NG-5400 MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000181 +name: OMEGA +def: "IonSpec OMEGA MS." [PSI:MS] +is_a: MS:1000123 ! IonSpec instrument model + +[Term] +id: MS:1000182 +name: OMEGA-2001 +def: "IonSpec OMEGA-2001 MS." [PSI:MS] +is_a: MS:1000123 ! IonSpec instrument model + +[Term] +id: MS:1000183 +name: OmniFlex +def: "Bruker Daltonics' OmniFlex: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000184 +name: Platform ICP +def: "Waters Platform ICP MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000185 +name: PolarisQ +def: "ThermoFinnigan PolarisQ MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000186 +name: proteomics solution 1 +def: "Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000187 +name: Q TRAP +def: "Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000188 +name: Q-Tof micro +def: "Waters oa-ToF based Q-Tof micro." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000189 +name: Q-Tof Ultima +def: "Waters oa-ToF based Q-Tof Ultima." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000190 +name: QSTAR +def: "Applied Biosystems/MDS SCIEX QSTAR MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000191 +name: quattro micro +def: "Waters (triple) quadrupole based micro." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000192 +name: Quattro Ultima +def: "Waters (triple) quadrupole based Ultima." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000193 +name: Surveyor MSQ +def: "ThermoFinnigan Surveyor MSQ MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000194 +name: SymBiot I +def: "Applied Biosystems/MDS SCIEX SymBiot I MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000195 +name: SymBiot XVI +def: "Applied Biosystems/MDS SCIEX SymBiot XVI MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000196 +name: TEMPUS TOF +def: "ThermoFinnigan TEMPUS TOF MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000197 +name: TRACE DSQ +def: "ThermoFinnigan TRACE DSQ MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000198 +name: TRITON +def: "ThermoFinnigan TRITON MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000199 +name: TSQ Quantum +def: "ThermoFinnigan TSQ Quantum MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000200 +name: ultima +def: "IonSpec Ultima MS." [PSI:MS] +is_a: MS:1000123 ! IonSpec instrument model + +[Term] +id: MS:1000201 +name: ultraflex +def: "Bruker Daltonics' ultraflex: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000202 +name: ultraflex TOF/TOF +def: "Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000203 +name: Voyager-DE PRO +def: "Applied Biosystems/MDS SCIEX Voyager-DE PRO MS." [PSI:MS] +is_a: MS:1000495 ! Applied Biosystems instrument model + +[Term] +id: MS:1000204 +name: Voyager-DE STR +def: "Applied Biosystems/MDS SCIEX Voyager-DE STR MS." [PSI:MS] +is_a: MS:1000495 ! Applied Biosystems instrument model + +[Term] +id: MS:1000205 +name: selected ion monitoring +def: "The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum." [PSI:MS] +synonym: "MIM" RELATED [] +synonym: "Multiple Ion Monitoring" EXACT [] +synonym: "SIM" EXACT [] +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1000206 +name: selected reaction monitoring +def: "Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space." [PSI:MS] +synonym: "MRM" RELATED [] +synonym: "Multiple Reaction Monitoring" RELATED [] +synonym: "SRM" EXACT [] +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1000207 +name: accurate mass +def: "OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition." [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +relationship: has_units UO:0000002 ! mass unit +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000208 +name: average mass +def: "OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance." [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +relationship: has_units UO:0000002 ! mass unit +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000209 +name: appearance energy +def: "OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended." [PSI:MS] +synonym: "AE" EXACT [] +comment: This child of the former purgatory term ion attribute was made obsolete. +relationship: has_units UO:0000266 ! electronvolt +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000210 +name: base peak +def: "The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures." [PSI:MS] +synonym: "BP" EXACT [] +is_a: MS:1000231 ! peak + +[Term] +id: MS:1000211 +name: OBSOLETE charge number +def: "OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS] +is_obsolete: true +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1000212 +name: dalton +def: "OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg." [PSI:MS] +comment: This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221). +is_obsolete: true + +[Term] +id: MS:1000213 +name: electron affinity +def: "OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy." [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +synonym: "EA" EXACT [] +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000214 +name: electron energy obsolete +def: "OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000215 +name: exact mass +def: "OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom." [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +relationship: has_units UO:0000002 ! mass unit +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000216 +name: field-free region +def: "A section of a mass spectrometer in which there are no electric or magnetic fields." [PSI:MS] +synonym: "FFR" EXACT [] +is_a: MS:1000487 ! ion optics attribute + +[Term] +id: MS:1000217 +name: ionization cross section +def: "OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000218 +name: ionization efficiency +def: "OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] +comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392). +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000219 +name: ionization energy +def: "OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS] +synonym: "IE" EXACT [] +comment: This child of the former purgatory term ion attribute was made obsolete. +relationship: has_units UO:0000266 ! electronvolt +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000220 +name: isotope dilution mass spectrometry +def: "OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard." [PSI:MS] +comment: This child of the former purgatory term mass spectrometry was made obsolete. +synonym: "IDMS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000221 +name: magnetic deflection +def: "The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer." [PSI:MS] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000222 +name: mass defect +def: "OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom." [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +relationship: has_units UO:0000002 ! mass unit +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000223 +name: mass number +def: "OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +is_obsolete: true +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1000224 +name: molecular mass +def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass] +is_a: MS:1000861 ! molecular entity property +relationship: has_units UO:0000002 ! mass unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000225 +name: monoisotopic mass +def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element." [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +relationship: has_units UO:0000002 ! mass unit +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000226 +name: molecular beam mass spectrometry +def: "OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "MBMS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000227 +name: multiphoton ionization +def: "Photoionization of an atom or molecule in which in two or more photons are absorbed." [PSI:MS] +synonym: "MPI" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000228 +name: nitrogen rule +def: "OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000229 +name: nominal mass +def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value." [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +relationship: has_units UO:0000002 ! mass unit +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000230 +name: odd-electron rule +def: "OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000231 +name: peak +def: "A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1000232 +name: peak intensity +def: "OBSOLETE The height or area of a peak in a mass spectrum." [PSI:MS] +comment: This term was made obsolete because it was replaced by base peak intensity (MS:1000505). +is_obsolete: true + +[Term] +id: MS:1000233 +name: proton affinity +def: "OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states." [PSI:MS] +synonym: "PA" EXACT [PSI:MS] +comment: This child of the former purgatory term ion attribute was made obsolete. +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000234 +name: mass resolving power +def: "OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS] +comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800). +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000235 +name: total ion current chromatogram +def: "Representation of the total ion current detected in each of a series of mass spectra versus time." [PSI:MS] +synonym: "TIC chromatogram" EXACT [] +is_a: MS:1000810 ! ion current chromatogram + +[Term] +id: MS:1000236 +name: transmission +def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS] +is_a: MS:1000496 ! instrument attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000237 +name: unified atomic mass unit +def: "OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg." [PSI:MS] +comment: This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221). +synonym: "u" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000238 +name: accelerator mass spectrometry +def: "OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "AMS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000239 +name: atmospheric pressure matrix-assisted laser desorption ionization +def: "Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer." [PSI:MS] +synonym: "AP MALDI" EXACT [] +is_a: MS:1000240 ! atmospheric pressure ionization + +[Term] +id: MS:1000240 +name: atmospheric pressure ionization +def: "Any ionization process in which ions are formed in the gas phase at atmospheric pressure." [PSI:MS] +synonym: "API" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000241 +name: Atmostpheric Pressure Photoionization +def: "OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS] +comment: This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382). +synonym: "APPI" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000242 +name: blackbody infrared radiative dissociation +def: "A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation." [PSI:MS] +synonym: "BIRD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000243 +name: charge-remote fragmentation +def: "OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +synonym: "CRF" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000244 +name: consecutive reaction monitoring +def: "OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] +comment: This former purgatory term was made obsolete. +synonym: "CRM" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000245 +name: charge stripping +def: "The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion." [PSI:MS] +synonym: "CS" EXACT [] +is_a: MS:1000510 ! precursor activation attribute + +[Term] +id: MS:1000246 +name: delayed extraction +def: "The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer." [PSI:MS] +synonym: "DE" EXACT [] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000247 +name: desorption ionization +def: "The formation of ions from a solid or liquid material after the rapid vaporization of that sample." [PSI:MS] +synonym: "DI" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000248 +name: direct insertion probe +def: "A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization." [PSI:MS] +synonym: "DIP" EXACT [] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000249 +name: direct liquid introduction +def: "The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization." [PSI:MS] +synonym: "DLI" EXACT [] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000250 +name: electron capture dissociation +def: "A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments." [PSI:MS] +synonym: "ECD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000251 +name: even-electron ion +def: "OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +synonym: "EE" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000252 +name: electron-induced excitation in organics +def: "OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +synonym: "EIEIO" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000253 +name: electron multiplier +def: "A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons." [PSI:MS] +synonym: "EM" EXACT [] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000254 +name: electrostatic energy analyzer +def: "A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time." [PSI:MS] +synonym: "ESA" EXACT [] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000255 +name: flowing afterglow +def: "An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa." [PSI:MS] +synonym: "FA" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000256 +name: high-field asymmetric waveform ion mobility spectrometry +def: "OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "FAIMS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000257 +name: field desorption +def: "The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization." [PSI:MS] +synonym: "FD" EXACT [] +is_a: MS:1000247 ! desorption ionization + +[Term] +id: MS:1000258 +name: field ionization +def: "The removal of electrons from any species by interaction with a high electric field." [PSI:MS] +synonym: "FI" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000259 +name: glow discharge ionization +def: "The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas." [PSI:MS] +synonym: "GD-MS" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000260 +name: ion kinetic energy spectrometry +def: "OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "IKES" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000261 +name: ion mobility spectrometry +def: "OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "IMS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000262 +name: infrared multiphoton dissociation +def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons." [PSI:MS] +synonym: "IRMPD" EXACT [] +is_a: MS:1000435 ! photodissociation + +[Term] +id: MS:1000263 +name: isotope ratio mass spectrometry +def: "OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer." [PSI:MS] +comment: This child of the former purgatory term mass spectrometry was made obsolete. +synonym: "IRMS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000264 +name: ion trap +def: "A device for spatially confining ions using electric and magnetic fields alone or in combination." [PSI:MS] +synonym: "IT" EXACT [] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000265 +name: kinetic energy release distribution +def: "OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +synonym: "KERD" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000266 +name: Laser Desorption +def: "OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules." [PSI:MS] +comment: This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393). +synonym: "Laser Ionization MERGE" EXACT [] +synonym: "LD" EXACT [] +is_obsolete: true +replaced_by: MS:1000393 + +[Term] +id: MS:1000267 +name: mass analyzed ion kinetic energy spectrometry +def: "OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "MIKES" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000268 +name: mass spectrometry +def: "OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments." [PSI:MS] +comment: This former purgatory term was made obsolete. +synonym: "MS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000269 +name: mass spectrometry/mass spectrometry +def: "OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "MS/MS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000270 +name: multiple stage mass spectrometry +def: "OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +synonym: "MSn" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000271 +name: Negative Ion chemical ionization +def: "Chemical ionization that results in the formation of negative ions." [PSI:MS] +synonym: "NICI" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000272 +name: neutralization reionization mass spectrometry +def: "With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species." [PSI:MS] +synonym: "NRMS" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000273 +name: photoionization +def: "The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended." [PSI:MS] +synonym: "PI" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000274 +name: pyrolysis mass spectrometry +def: "A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source." [PSI:MS] +synonym: "PyMS" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000275 +name: collision quadrupole +def: "A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation." [PSI:MS] +synonym: "q" EXACT [] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000276 +name: resonance enhanced multiphoton ionization +def: "Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species." [PSI:MS] +synonym: "REMPI" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000277 +name: residual gas analyzer +def: "OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "RGA" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000278 +name: surface enhanced laser desorption ionization +def: "The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization." [PSI:MS] +synonym: "SELDI" EXACT [] +is_a: MS:1000406 ! surface ionization + +[Term] +id: MS:1000279 +name: surface enhanced neat desorption +def: "Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface." [PSI:MS] +synonym: "SEND" EXACT [] +is_a: MS:1000406 ! surface ionization + +[Term] +id: MS:1000280 +name: suface ionization +def: "OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS] +comment: This term was made obsolete because it was replaced by surface ionization (MS:1000406). +synonym: "SI" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000281 +name: selected ion flow tube +def: "A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions." [PSI:MS] +synonym: "SIFT" EXACT [] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000282 +name: sustained off-resonance irradiation +def: "A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time." [PSI:MS] +synonym: "SORI" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000283 +name: Spark Source Mass Spectrometry +def: "OBSOLETE Mass spectrometry using spark ionization." [PSI:MS] +comment: This term was made obsolete because it was replaced by spark ionization (MS:1000404). +synonym: "SSMS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000284 +name: stored waveform inverse fourier transform +def: "A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments." [PSI:MS] +synonym: "SWIFT" EXACT [] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000285 +name: total ion current +def: "The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum." [PSI:MS] +synonym: "TIC" EXACT [] +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000286 +name: time lag focusing +def: "Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse." [PSI:MS] +synonym: "TLF" EXACT [] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000287 +name: time-of-flight mass spectrometer +def: "OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +synonym: "TOF-MS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000288 +name: cyclotron +def: "A device that uses an oscillating electric field and magnetic field to accelerate charged particles." [PSI:MS] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000289 +name: double-focusing mass spectrometer +def: "OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000290 +name: hybrid mass spectrometer +def: "OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000291 +name: linear ion trap +def: "A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap." [PSI:MS] +is_a: MS:1000264 ! ion trap + +[Term] +id: MS:1000292 +name: mass spectrograph obsolete +def: "OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000293 +name: mass spectrometer +def: "OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000294 +name: mass spectrum +def: "A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z)." [PSI:MS] +is_a: MS:1000524 ! data file content +is_a: MS:1000559 ! spectrum type + +[Term] +id: MS:1000295 +name: mattauch-herzog geometry +def: "OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000296 +name: nier-johnson geometry +def: "OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000297 +name: paul ion trap +def: "OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected." [PSI:MS] +comment: This term was made obsolete because it is redundant to quadrupole ion trap. +synonym: "quadrupole ion trap" RELATED [] +is_obsolete: true + +[Term] +id: MS:1000298 +name: prolate traochoidal mass spectrometer +def: "OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000299 +name: quistor +def: "OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000300 +name: reflectron +def: "A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time." [PSI:MS] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000301 +name: sector mass spectrometer +def: "OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000302 +name: tandem mass spectrometer +def: "OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000303 +name: transmission quadrupole mass spectrometer +def: "OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000304 +name: accelerating voltage +def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] +is_a: MS:1000487 ! ion optics attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000305 +name: cyclotron motion +def: "OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000306 +name: dynamic mass spectrometry +def: "OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time." [PSI:MS] +comment: This child of the former purgatory term mass spectrometer was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000307 +name: einzel lens +def: "Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle." [PSI:MS] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000308 +name: electric field strength +def: "The magnitude of the force per unit charge at a given point in space." [PSI:MS] +is_a: MS:1000487 ! ion optics attribute +relationship: has_units UO:0000268 ! volt per meter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000309 +name: first stability region +def: "The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole." [PSI:MS] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000310 +name: fringing field +def: "The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element." [PSI:MS] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000311 +name: kinetic energy analyzer +def: "A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field." [PSI:MS] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000312 +name: mass limit +def: "OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000313 +name: scan m/z range? +def: "OBSOLETE The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000314 +name: mass selective axial ejection +def: "OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000315 +name: mass selective instability +def: "OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000316 +name: mathieu stability diagram +def: "OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000317 +name: orthogonal extraction +def: "OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000318 +name: resonance ion ejection +def: "OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000319 +name: space charge effect +def: "The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time." [PSI:MS] +is_a: MS:1000487 ! ion optics attribute + +[Term] +id: MS:1000320 +name: static field +def: "An electric or magnetic field that does not change in time." [PSI:MS] +is_a: MS:1000597 ! ion optics type + +[Term] +id: MS:1000321 +name: 2E Mass Spectrum +def: "OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000322 +name: charge inversion mass spectrum +def: "The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000323 +name: constant neutral loss scan +def: "OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement." [PSI:MS] +comment: This former purgatory term was made obsolete. +synonym: "constant neutral mass loss scan" RELATED [] +synonym: "fixed neutral fragment scan" RELATED [] +is_obsolete: true + +[Term] +id: MS:1000324 +name: constant neutral gain scan +def: "OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment." [PSI:MS] +comment: This former purgatory term was made obsolete. +synonym: "Constant Neutral Mass Gain Scan" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000325 +name: constant neutral gain spectrum +def: "A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell." [PSI:MS] +synonym: "constant neutral mass gain spectrum" EXACT [] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000326 +name: constant neutral loss spectrum +def: "A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS] +synonym: "constant neutral mass loss spectrum" EXACT [] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000327 +name: consecutive reaction monitoring +def: "OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] +comment: This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244). +is_obsolete: true + +[Term] +id: MS:1000328 +name: e/2 mass spectrum +def: "A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions." [PSI:MS] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000329 +name: linked scan +def: "OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000330 +name: linked scan at constant b/e +def: "OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors." [PSI:MS] +comment: This child of the former purgatory term linked scan was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000331 +name: Linked Scan at Constant E2/V +def: "OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors." [PSI:MS] +comment: This child of the former purgatory term linked scan was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000332 +name: Linked Scan at Constant B2/E +def: "OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended." [PSI:MS] +comment: This child of the former purgatory term linked scan was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000333 +name: Linked Scan at Constant B[1-(E/E0)]^1/2 / E +def: "OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan." [PSI:MS] +comment: This child of the former purgatory term linked scan was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000334 +name: MS/MS in Time +def: "OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000335 +name: MS/MS in Space +def: "OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition." [PSI:MS] +comment: This child of the former purgatory term m/z Separation Method was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000336 +name: neutral loss +def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS] +is_a: MS:1001055 ! modification parameters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000337 +name: nth generation product ion +def: "OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated." [PSI:MS] +comment: This child of the former purgatory term product ion was made obsolete. +synonym: "granddaughter ion" RELATED [] +is_obsolete: true + +[Term] +id: MS:1000338 +name: nth generation product ion scan +def: "OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000339 +name: nth generation product ion spectrum +def: "OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions." [PSI:MS] +comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580). +is_obsolete: true + +[Term] +id: MS:1000340 +name: precursor ion +def: "OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated." [PSI:MS] +comment: This child of the former purgatory term ion role was made obsolete. +synonym: "parent ion" RELATED [] +is_obsolete: true + +[Term] +id: MS:1000341 +name: precursor ion spectrum +def: "Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z." [PSI:MS] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000342 +name: product ion +def: "OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated." [PSI:MS] +comment: This child of the former purgatory term ion role was made obsolete. +synonym: "daughter ion" RELATED [] +is_obsolete: true + +[Term] +id: MS:1000343 +name: product ion spectrum +def: "OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions." [PSI:MS] +comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580). +is_a: MS:1000294 ! mass spectrum +is_obsolete: true + +[Term] +id: MS:1000344 +name: progeny ion +def: "OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +synonym: "Progeny Fragment Ion" EXACT [] +is_obsolete: true + +[Term] +id: MS:1000345 +name: array detector +def: "Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000346 +name: conversion dynode +def: "A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000347 +name: dynode +def: "One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000348 +name: focal plane collector +def: "A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000349 +name: ion-to-photon detector +def: "A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000350 +name: point collector +def: "A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000351 +name: postacceleration detector +def: "A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000352 +name: secondary electron +def: "OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000353 +name: adduct ion +def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS] +is_a: MS:1003055 ! adduct + +[Term] +id: MS:1000354 +name: aromatic ion +def: "OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000355 +name: analog ion +def: "OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000356 +name: anti-aromatic ion +def: "OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000357 +name: cationized molecule +def: "OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000358 +name: cluster ion +def: "OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000359 +name: Conventional ion +def: "OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000360 +name: diagnostic ion +def: "OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000361 +name: dimeric ion +def: "OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000362 +name: distonic ion +def: "OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000363 +name: enium ion +def: "OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000364 +name: fragment ion +def: "OBSOLETE A product ion that results from the dissociation of a precursor ion." [PSI:MS] +comment: This term was made obsolete because it was replaced by product ion (MS:1000342). +is_obsolete: true + +[Term] +id: MS:1000365 +name: ion? +def: "OBSOLETE An atomic or molecular species having a net positive or negative electric charge." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000366 +name: Isotopologue ion +def: "OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000367 +name: Isotopomeric ion +def: "OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000368 +name: metastable ion +def: "OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection." [PSI:MS] +comment: This child of the former purgatory term ion stability type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000369 +name: molecular ion +def: "OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000370 +name: negative ion +def: "OBSOLETE An atomic or molecular species having a net negative electric charge." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000371 +name: non-classical ion +def: "OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000372 +name: onium ion +def: "OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000373 +name: principal ion +def: "OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000374 +name: positive ion +def: "OBSOLETE An atomic or molecular species having a net positive electric charge." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000375 +name: protonated molecule +def: "OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000376 +name: radical ion +def: "OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000377 +name: reference ion +def: "OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion." [PSI:MS] +comment: This child of the former purgatory term ion chemical type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000378 +name: stable ion +def: "OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer." [PSI:MS] +comment: This child of the former purgatory term ion stability type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000379 +name: unstable ion +def: "OBSOLETE An ion with sufficient energy to dissociate within the ion source." [PSI:MS] +comment: This child of the former purgatory term ion stability type was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000380 +name: adiabatic ionization +def: "A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000381 +name: associative ionization +def: "An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000382 +name: atmospheric pressure photoionization +def: "Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS] +is_a: MS:1000240 ! atmospheric pressure ionization + +[Term] +id: MS:1000383 +name: autodetachment +def: "The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000384 +name: autoionization +def: "The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000385 +name: charge exchange ionization +def: "The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000386 +name: chemi-ionization +def: "The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000387 +name: desorption/ionization on silicon +def: "The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface." [PSI:MS] +is_a: MS:1000247 ! desorption ionization + +[Term] +id: MS:1000388 +name: dissociative ionization +def: "The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000389 +name: electron ionization +def: "The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000390 +name: ion desolvation +def: "OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000391 +name: ion-pair formation +def: "OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000392 +name: ionization efficiency +def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] +is_a: MS:1000482 ! source attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000393 +name: laser desorption ionization +def: "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS] +is_a: MS:1000247 ! desorption ionization + +[Term] +id: MS:1000395 +name: liquid secondary ionization +def: "The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000396 +name: membrane inlet +def: "A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source." [PSI:MS] +is_a: MS:1000007 ! inlet type + +[Term] +id: MS:1000397 +name: microelectrospray +def: "Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray." [PSI:MS] +is_a: MS:1000073 ! electrospray ionization + +[Term] +id: MS:1000398 +name: nanoelectrospray +def: "Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray." [PSI:MS] +synonym: "nanospray" EXACT [] +is_a: MS:1000073 ! electrospray ionization + +[Term] +id: MS:1000399 +name: penning ionization +def: "Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000400 +name: plasma desorption ionization +def: "The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000401 +name: pre-ionization state +def: "OBSOLETE An electronic state capable of undergoing auto-Ionization." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000402 +name: secondary ionization +def: "The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000403 +name: soft ionization +def: "The formation of gas-phase ions without extensive fragmentation." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000404 +name: spark ionization +def: "The formation of ions from a solid material by an intermittent electrical discharge." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000405 +name: surface-assisted laser desorption ionization +def: "The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization." [PSI:MS] +is_a: MS:1000247 ! desorption ionization + +[Term] +id: MS:1000406 +name: surface ionization +def: "The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000407 +name: thermal ionization +def: "The ionization of a neutral species through contact with a high temperature surface." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000408 +name: vertical ionization +def: "A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000409 +name: association reaction +def: "OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000410 +name: alpha-cleavage +def: "OBSOLETE A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000411 +name: beta-cleavage +def: "OBSOLETE A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000412 +name: buffer gas +def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000413 +name: charge-induced fragmentation +def: "OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000414 +name: charge inversion reaction +def: "OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000415 +name: charge permutation reaction +def: "OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000416 +name: charge stripping reaction +def: "OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000417 +name: charge transfer reaction +def: "OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000418 +name: collisional excitation +def: "OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000419 +name: collision gas +def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000420 +name: heterolytic cleavage +def: "OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +synonym: "heterolysis" RELATED [] +is_obsolete: true + +[Term] +id: MS:1000421 +name: high energy collision +def: "OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000422 +name: beam-type collision-induced dissociation +def: "A collision-induced dissociation process that occurs in a beam-type collision cell." [PSI:MS] +synonym: "HCD" EXACT [] +is_a: MS:1000133 ! collision-induced dissociation + +[Term] +id: MS:1000423 +name: homolytic cleavage +def: "OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +synonym: "homolysis" RELATED [] +is_obsolete: true + +[Term] +id: MS:1000424 +name: hydrogen/deuterium exchange +def: "OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000425 +name: ion energy loss spectrum +def: "OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000426 +name: ionizing collision +def: "OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000427 +name: ion/molecule reaction +def: "OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000428 +name: ion/neutral complex +def: "OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000429 +name: ion/neutral species reaction +def: "OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000430 +name: ion/neutral species exchange reaction +def: "OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000431 +name: kinetic method +def: "OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000432 +name: low energy collisions +def: "OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000433 +name: low-energy collision-induced dissociation +def: "A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative." [PSI:MS] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000434 +name: McLafferty Rearrangement +def: "OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000435 +name: photodissociation +def: "A process wherein the reactant ion is dissociated as a result of absorption of one or more photons." [PSI:MS] +synonym: "multiphoton dissociation" EXACT [] +synonym: "MPD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000436 +name: partial charge transfer reaction +def: "OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000437 +name: ion reaction +def: "OBSOLETE Chemical transformation involving an ion." [PSI:MS] +comment: This child of the former purgatory term ion was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000438 +name: superelastic collision +def: "OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000439 +name: surface-induced reaction +def: "OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000440 +name: unimolecular dissociation +def: "OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion." [PSI:MS] +comment: This child of the former purgatory term ion reaction was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000441 +name: scan +def: "Function or process of the mass spectrometer where it records a spectrum." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000442 +name: spectrum +def: "Representation of intensity values corresponding to a range of measurement space." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000443 +name: mass analyzer type +def: "Mass analyzer separates the ions according to their mass-to-charge ratio." [PSI:MS] +relationship: part_of MS:1000451 ! mass analyzer + +[Term] +id: MS:1000444 +name: m/z Separation Method +def: "OBSOLETE Mass/charge separation Method." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000445 +name: sequential m/z separation method +def: "OBSOLETE Sequential m/z separation method." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000446 +name: fast ion bombardment +def: "The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample." [PSI:MS] +synonym: "FIB" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1000447 +name: LTQ +def: "Finnigan LTQ MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000448 +name: LTQ FT +def: "Finnigan LTQ FT MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000449 +name: LTQ Orbitrap +def: "Finnigan LTQ Orbitrap MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000450 +name: LXQ +def: "Finnigan LXQ MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000451 +name: mass analyzer +def: "Terms used to describe the Analyzer." [PSI:MS] +synonym: "analyzer" EXACT [] +relationship: part_of MS:1000463 ! instrument + +[Term] +id: MS:1000452 +name: data transformation +def: "Terms used to describe types of data processing." [PSI:MS] +synonym: "data processing" EXACT [] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000453 +name: detector +def: "The device that detects ions." [PSI:MS] +relationship: part_of MS:1000463 ! instrument + +[Term] +id: MS:1000454 +name: instrument additional description +def: "OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000455 +name: ion selection attribute +def: "Ion selection properties that are associated with a value." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1000456 +name: precursor activation +def: "Terms to describe the precursor activation." [PSI:MS] +synonym: "activation" EXACT [] +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1000457 +name: sample +def: "Terms to describe the sample." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000458 +name: source +def: "Terms to describe the source." [PSI:MS] +relationship: part_of MS:1000463 ! instrument + +[Term] +id: MS:1000459 +name: spectrum instrument description +def: "OBSOLETE Terms used to describe the spectrum." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000460 +name: unit +def: "OBSOLETE Terms to describe units." [PSI:MS] +comment: This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000). +relationship: part_of MS:1001458 ! spectrum generation information +is_obsolete: true + +[Term] +id: MS:1000461 +name: additional description +def: "OBSOLETE Terms to describe Additional." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000462 +name: ion optics +def: "Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions." [PSI:MS] +relationship: part_of MS:1000463 ! instrument + +[Term] +id: MS:1000463 +name: instrument +def: "Description of the instrument or the mass spectrometer." [PSI:MS] +synonym: "instrument configuration" EXACT [] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000464 +name: mass unit +def: "OBSOLETE A unit of measurement for mass." [PSI:MS] +comment: This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002). +is_obsolete: true + +[Term] +id: MS:1000465 +name: scan polarity +def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS] +relationship: part_of MS:1000441 ! scan + +[Term] +id: MS:1000466 +name: alternating +def: "OBSOLETE Alternating." [PSI:MS] +comment: This term was made obsolete because . +is_obsolete: true + +[Term] +id: MS:1000467 +name: 1200 series LC/MSD SL +def: "The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000468 +name: 6110 Quadrupole LC/MS +def: "The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000469 +name: 6120A Quadrupole LC/MS +def: "The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000470 +name: 6130 Quadrupole LC/MS +def: "The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000471 +name: 6140 Quadrupole LC/MS +def: "The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000472 +name: 6210 Time-of-Flight LC/MS +def: "The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000473 +name: 6310 Ion Trap LC/MS +def: "The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000474 +name: 6320 Ion Trap LC/MS +def: "The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000475 +name: 6330 Ion Trap LC/MS +def: "The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000476 +name: 6340 Ion Trap LC/MS +def: "The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000477 +name: 6410 Triple Quadrupole LC/MS +def: "The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration." [PSI:MS] +synonym: "6410 Triple Quad LC/MS" EXACT [] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000478 +name: 1200 series LC/MSD VL +def: "The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000479 +name: purgatory +def: "OBSOLETE Terms that will likely become obsolete unless there are wails of dissent." [PSI:MS] +comment: The whole branch purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000480 +name: mass analyzer attribute +def: "Analyzer properties that are associated with a value." [PSI:MS] +relationship: part_of MS:1000451 ! mass analyzer + +[Term] +id: MS:1000481 +name: detector attribute +def: "Detector attribute recognized as a value." [PSI:MS] +relationship: part_of MS:1000453 ! detector + +[Term] +id: MS:1000482 +name: source attribute +def: "Property of a source device that need a value." [PSI:MS] +relationship: part_of MS:1000458 ! source + +[Term] +id: MS:1000483 +name: Thermo Fisher Scientific instrument model +def: "Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific." [PSI:MS] +synonym: "Thermo Scientific" RELATED [] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000484 +name: orbitrap +def: "An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer." [PSI:MS] +is_a: MS:1000443 ! mass analyzer type + +[Term] +id: MS:1000485 +name: nanospray inlet +def: "Nanospray Inlet." [PSI:MS] +is_a: MS:1000057 ! electrospray inlet + +[Term] +id: MS:1000486 +name: source potential +def: "Potential difference at the MS source in volts." [PSI:MS] +is_a: MS:1000482 ! source attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000487 +name: ion optics attribute +def: "Ion optics involves components that help focus ion streams in mass spectrometry." [PSI:MS] +is_a: MS:1000462 ! ion optics + +[Term] +id: MS:1000488 +name: Hitachi instrument model +def: "Hitachi instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000489 +name: Varian instrument model +def: "Varian instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000490 +name: Agilent instrument model +def: "Agilent instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000491 +name: Dionex instrument model +def: "Dionex instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000492 +name: Thermo Electron instrument model +def: "Thermo Electron Corporation instrument model." [PSI:MS] +is_a: MS:1000483 ! Thermo Fisher Scientific instrument model + +[Term] +id: MS:1000493 +name: Finnigan MAT instrument model +def: "Finnigan MAT instrument model." [PSI:MS] +is_a: MS:1000483 ! Thermo Fisher Scientific instrument model + +[Term] +id: MS:1000494 +name: Thermo Scientific instrument model +def: "Thermo Scientific instrument model." [PSI:MS] +is_a: MS:1000483 ! Thermo Fisher Scientific instrument model + +[Term] +id: MS:1000495 +name: Applied Biosystems instrument model +def: "Applied Biosystems instrument model." [PSI:MS] +synonym: "ABI" EXACT [] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1000496 +name: instrument attribute +def: "Instrument properties that are associated with a value." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000463 ! instrument + +[Term] +id: MS:1000497 +name: zoom scan +def: "Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS] +synonym: "enhanced resolution scan" EXACT [] +is_a: MS:1000503 ! scan attribute + +[Term] +id: MS:1000498 +name: full scan +def: "OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000499 +name: spectrum attribute +def: "Nonphysical characteristic attributed to a spectrum." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1000500 +name: scan window upper limit +def: "The lower m/z bound of a mass spectrometer scan window." [PSI:MS] +synonym: "mzRangeStop" RELATED [] +is_a: MS:1000549 ! selection window attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000501 +name: scan window lower limit +def: "The upper m/z bound of a mass spectrometer scan window." [PSI:MS] +synonym: "mzRangeStart" RELATED [] +is_a: MS:1000549 ! selection window attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000502 +name: dwell time +def: "The time spent gathering data across a peak." [PSI:MS] +synonym: "Scan Duration" RELATED [] +is_a: MS:1000503 ! scan attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000503 +name: scan attribute +def: "Nonphysical characteristic attributed to a spectrum acquisition scan." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000441 ! scan + +[Term] +id: MS:1000504 +name: base peak m/z +def: "M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS] +is_a: MS:1003058 ! spectrum property +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000505 +name: base peak intensity +def: "The intensity of the greatest peak in the mass spectrum." [PSI:MS] +is_a: MS:1003058 ! spectrum property +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 +relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000506 +name: ion role +def: "OBSOLETE Ion Role." [PSI:MS] +comment: This child of the former purgatory term ion was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000507 +name: ion property +def: "Nonphysical characteristic attributed to an ion." [PSI:MS] +relationship: part_of MS:1002806 ! ion + +[Term] +id: MS:1000508 +name: ion chemical type +def: "OBSOLETE Ion Type." [PSI:MS] +comment: This child of the former purgatory term ion was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000509 +name: activation energy +def: "Activation Energy." [PSI:MS] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000510 +name: precursor activation attribute +def: "Precursor Activation Attribute." [PSI:MS] +relationship: part_of MS:1000456 ! precursor activation + +[Term] +id: MS:1000511 +name: ms level +def: "Stage number achieved in a multi stage mass spectrometry acquisition." [PSI:MS] +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1000512 +name: filter string +def: "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000513 +name: binary data array +def: "A data array of values." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum +relationship: part_of MS:1000625 ! chromatogram + +[Term] +id: MS:1000514 +name: m/z array +def: "A data array of m/z values." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units MS:1000040 ! m/z + +[Term] +id: MS:1000515 +name: intensity array +def: "A data array of intensity values." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 +relationship: has_units UO:0000269 ! absorbance unit + +[Term] +id: MS:1000516 +name: charge array +def: "A data array of charge values." [PSI:MS] +xref: binary-data-type:MS\:1000519 "32-bit integer" +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1000517 +name: signal to noise array +def: "A data array of signal-to-noise values." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1000518 +name: binary data type +def: "Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum +relationship: part_of MS:1000625 ! chromatogram + +[Term] +id: MS:1000519 +name: 32-bit integer +def: "Signed 32-bit little-endian integer." [PSI:MS] +is_a: MS:1000518 ! binary data type + +[Term] +id: MS:1000520 +name: 16-bit float +def: "OBSOLETE Signed 16-bit float." [PSI:MS] +is_a: MS:1000518 ! binary data type +is_obsolete: true + +[Term] +id: MS:1000521 +name: 32-bit float +def: "32-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS] +is_a: MS:1000518 ! binary data type + +[Term] +id: MS:1000522 +name: 64-bit integer +def: "Signed 64-bit little-endian integer." [PSI:MS] +is_a: MS:1000518 ! binary data type + +[Term] +id: MS:1000523 +name: 64-bit float +def: "64-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS] +is_a: MS:1000518 ! binary data type + +[Term] +id: MS:1000524 +name: data file content +def: "Describes the data content on the file." [PSI:MS] +relationship: part_of MS:1000577 ! source data file + +[Term] +id: MS:1000525 +name: spectrum representation +def: "Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1000526 +name: Waters raw format +def: "Waters data file format found in a Waters RAW directory, generated from an MS acquisition." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000527 +name: highest observed m/z +def: "Highest m/z value observed in the m/z array." [PSI:MS] +is_a: MS:1000808 ! chromatogram attribute +is_a: MS:1003058 ! spectrum property +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000528 +name: lowest observed m/z +def: "Lowest m/z value observed in the m/z array." [PSI:MS] +is_a: MS:1000808 ! chromatogram attribute +is_a: MS:1003058 ! spectrum property +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000529 +name: instrument serial number +def: "Serial Number of the instrument." [PSI:MS] +is_a: MS:1000496 ! instrument attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000530 +name: file format conversion +def: "Conversion of one file format to another." [PSI:MS] +is_a: MS:1000452 ! data transformation + +[Term] +id: MS:1000531 +name: software +def: "Software related to the recording or transformation of spectra." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1000532 +name: Xcalibur +def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000693 ! Thermo Finnigan software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000533 +name: Bioworks +def: "Thermo Finnigan software for data analysis of peptides and proteins." [PSI:MS] +synonym: "Bioworks Browser" RELATED [] +is_a: MS:1000693 ! Thermo Finnigan software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000534 +name: MassLynx +def: "Micromass software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000694 ! Waters software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000535 +name: FlexAnalysis +def: "Bruker software for data analysis." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000536 +name: Data Explorer +def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000691 ! Applied Biosystems software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000537 +name: 4700 Explorer +def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000691 ! Applied Biosystems software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000538 +name: massWolf +def: "A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology." [PSI:MS] +synonym: "wolf" EXACT [] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000539 +name: Voyager Biospectrometry Workstation System +def: "Applied Biosystems MALDI-TOF data acquisition and analysis system." [PSI:MS] +is_a: MS:1000691 ! Applied Biosystems software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000540 +name: FlexControl +def: "Bruker software for data acquisition." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000541 +name: ReAdW +def: "A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced \"readraw\"." [PSI:MS] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000542 +name: MzStar +def: "A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program." [PSI:MS] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000543 +name: data processing action +def: "Data processing attribute used to describe the type of data processing performed on the data file." [PSI:MS] +is_a: MS:1000452 ! data transformation + +[Term] +id: MS:1000544 +name: Conversion to mzML +def: "Conversion of a file format to Proteomics Standards Initiative mzML file format." [PSI:MS] +is_a: MS:1000530 ! file format conversion + +[Term] +id: MS:1000545 +name: Conversion to mzXML +def: "Conversion of a file format to Institute of Systems Biology mzXML file format." [PSI:MS] +is_a: MS:1000530 ! file format conversion + +[Term] +id: MS:1000546 +name: Conversion to mzData +def: "Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS] +is_a: MS:1000530 ! file format conversion + +[Term] +id: MS:1000547 +name: object attribute +def: "Object Attribute." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000548 +name: sample attribute +def: "Sample properties that are associated with a value." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000457 ! sample + +[Term] +id: MS:1000549 +name: selection window attribute +def: "Selection window properties that are associated with a value." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000441 ! scan + +[Term] +id: MS:1000550 +name: time unit +def: "OBSOLETE Time Unit." [PSI:MS] +comment: This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003). +is_obsolete: true + +[Term] +id: MS:1000551 +name: Analyst +def: "SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000552 +name: maldi spot identifier +def: "OBSOLETE Maldi Spot Identifier." [PSI:MS] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1000553 +name: Trapper +def: "A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology." [PSI:MS] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000554 +name: LCQ Deca +def: "ThermoFinnigan LCQ Deca." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000555 +name: LTQ Orbitrap Discovery +def: "LTQ Orbitrap Discovery." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000556 +name: LTQ Orbitrap XL +def: "LTQ Orbitrap XL." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000557 +name: LTQ FT Ultra +def: "LTQ FT Ultra." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000558 +name: GC Quantum +def: "GC Quantum." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000559 +name: spectrum type +def: "Spectrum type." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1000560 +name: mass spectrometer file format +def: "The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:MS] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1000561 +name: data file checksum type +def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS] +relationship: part_of MS:1000577 ! source data file + +[Term] +id: MS:1000562 +name: ABI WIFF format +def: "Applied Biosystems WIFF file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000563 +name: Thermo RAW format +def: "Thermo Scientific RAW file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000564 +name: PSI mzData format +def: "Proteomics Standards Inititative mzData file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000565 +name: Micromass PKL format +def: "Micromass PKL file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000566 +name: ISB mzXML format +def: "Institute of Systems Biology mzXML file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000567 +name: Bruker/Agilent YEP format +def: "Bruker/Agilent YEP file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000568 +name: MD5 +def: "MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS] +is_a: MS:1000561 ! data file checksum type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000569 +name: SHA-1 +def: "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard." [PSI:MS] +is_a: MS:1000561 ! data file checksum type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000570 +name: spectra combination +def: "Method used to combine the mass spectra." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1000571 +name: sum of spectra +def: "Spectra Sum." [PSI:MS] +is_a: MS:1000570 ! spectra combination + +[Term] +id: MS:1000572 +name: binary data compression type +def: "Compression Type." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum +relationship: part_of MS:1000625 ! chromatogram + +[Term] +id: MS:1000573 +name: median of spectra +def: "Spectra is combined by calculating the median of the spectra." [PSI:MS] +is_a: MS:1000570 ! spectra combination + +[Term] +id: MS:1000574 +name: zlib compression +def: "Zlib." [PSI:MS] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1000575 +name: mean of spectra +def: "Spectra is combined by calculating the mean of the spectra." [PSI:MS] +is_a: MS:1000570 ! spectra combination + +[Term] +id: MS:1000576 +name: no compression +def: "No Compression." [PSI:MS] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1000577 +name: source data file +def: "Data file from which an entity is sourced." [PSI:MS] +synonym: "source file" EXACT [] +relationship: part_of MS:1001458 ! spectrum generation information +is_a: MS:1000499 ! spectrum attribute + +[Term] +id: MS:1000578 +name: LCQ Fleet +def: "LCQ Fleet." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000579 +name: MS1 spectrum +def: "Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment." [PSI:MS] +synonym: "full spectrum" EXACT [] +synonym: "Q1 spectrum" EXACT [] +synonym: "Q3 spectrum" EXACT [] +synonym: "Single-Stage Mass Spectrometry" EXACT [] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000580 +name: MSn spectrum +def: "MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n." [PSI:MS] +synonym: "multiple-stage mass spectrometry spectrum" EXACT [] +synonym: "nth generation product ion spectrum" EXACT [] +synonym: "product ion spectrum" EXACT [] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000581 +name: CRM spectrum +def: "Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000582 +name: SIM spectrum +def: "Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring)." [PSI:MS] +synonym: "MIM spectrum" EXACT [] +synonym: "multiple ion monitoring spectrum" EXACT [] +synonym: "selected ion monitoring spectrum" EXACT [] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000583 +name: SRM spectrum +def: "Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space." [PSI:MS] +synonym: "MRM spectrum" EXACT [] +synonym: "multiple reaction monitoring spectrum" EXACT [] +synonym: "selected reaction monitoring spectrum" EXACT [] +is_a: MS:1000294 ! mass spectrum + +[Term] +id: MS:1000584 +name: mzML format +def: "Proteomics Standards Inititative mzML file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000585 +name: contact attribute +def: "Details about a person or organization to contact in case of concern or discussion about the file." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1000586 +name: contact name +def: "Name of the contact person or organization." [PSI:MS] +is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000587 +name: contact address +def: "Postal address of the contact person or organization." [PSI:MS] +is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000588 +name: contact URL +def: "Uniform Resource Locator related to the contact person or organization." [PSI:MS] +is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000589 +name: contact email +def: "Email address of the contact person or organization." [PSI:MS] +is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000590 +name: contact affiliation +def: "Home institution of the contact person." [PSI:MS] +is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000591 +name: MzWiff +def: "A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program." [PSI:MS] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000592 +name: smoothing +def: "A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1000593 +name: baseline reduction +def: "A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1000594 +name: low intensity data point removal +def: "The removal of very low intensity data points that are likely to be spurious noise rather than real signal." [PSI:MS] +synonym: "thresholding" EXACT [] +is_a: MS:1001486 ! data filtering + +[Term] +id: MS:1000595 +name: time array +def: "A data array of relative time offset values from a reference time." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute + +[Term] +id: MS:1000596 +name: measurement method +def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000597 +name: ion optics type +def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] +is_a: MS:1000462 ! ion optics + +[Term] +id: MS:1000598 +name: electron transfer dissociation +def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions." [DOI:10.1073/pnas.0402700101, PMID:15210983, PSI:MS] +synonym: "ETD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000599 +name: pulsed q dissociation +def: "A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected." [PSI:MS] +synonym: "PQD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1000600 +name: Proteios +def: "Database application and analysis platform for proteomics." [PSI:MS, source:http://www.proteios.org] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000601 +name: ProteinLynx Global Server +def: "Waters software for data analysis." [PSI:MS] +is_a: MS:1000694 ! Waters software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000602 +name: Shimadzu MALDI-TOF instrument model +def: "Shimadzu MALDI-TOF instrument model." [PSI:MS] +is_a: MS:1000124 ! Shimadzu instrument model + +[Term] +id: MS:1000603 +name: Shimadzu Scientific Instruments instrument model +def: "Shimadzu Scientific Instruments instrument model." [PSI:MS] +is_a: MS:1000124 ! Shimadzu instrument model + +[Term] +id: MS:1000604 +name: LCMS-IT-TOF +def: "Shimadzu Scientific Instruments LCMS-IT-TOF MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1000605 +name: LCMS-2010EV +def: "Shimadzu Scientific Instruments LCMS-2010EV MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1000606 +name: LCMS-2010A +def: "Shimadzu Scientific Instruments LCMS-2010A MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1000607 +name: AXIMA CFR MALDI-TOF +def: "Shimadzu Biotech AXIMA CFR MALDI-TOF MS." [PSI:MS] +is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model + +[Term] +id: MS:1000608 +name: AXIMA-QIT +def: "Shimadzu Biotech AXIMA-QIT MS." [PSI:MS] +is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model + +[Term] +id: MS:1000609 +name: AXIMA-CFR plus +def: "Shimadzu Biotech AXIMA-CFR plus MS." [PSI:MS] +is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model + +[Term] +id: MS:1000610 +name: AXIMA Performance MALDI-TOF/TOF +def: "Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS." [PSI:MS] +is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model + +[Term] +id: MS:1000611 +name: AXIMA Confidence MALDI-TOF +def: "Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS." [PSI:MS] +is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model + +[Term] +id: MS:1000612 +name: AXIMA Assurance Linear MALDI-TOF +def: "Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS." [PSI:MS] +is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model + +[Term] +id: MS:1000613 +name: DTA format +def: "SEQUEST DTA file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000614 +name: ProteinLynx Global Server mass spectrum XML format +def: "Peak list file format used by ProteinLynx Global Server." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000615 +name: ProteoWizard software +def: "ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb." [PSI:MS] +synonym: "pwiz" EXACT [] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000616 +name: preset scan configuration +def: "A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000617 +name: wavelength array +def: "A data array of electromagnetic radiation wavelength values." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units UO:0000018 ! nanometer + +[Term] +id: MS:1000618 +name: highest observed wavelength +def: "Highest wavelength observed in an EMR spectrum." [PSI:MS] +is_a: MS:1003058 ! spectrum property +is_a: MS:1000808 ! chromatogram attribute +relationship: has_units UO:0000018 ! nanometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000619 +name: lowest observed wavelength +def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS] +is_a: MS:1003058 ! spectrum property +is_a: MS:1000808 ! chromatogram attribute +relationship: has_units UO:0000018 ! nanometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000620 +name: PDA spectrum +def: "OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum)." [PSI:MS] +comment: This term was made obsolete because it was replaced by absorption spectrum (MS:1000806). +is_a: MS:1000524 ! data file content +is_a: MS:1000559 ! spectrum type +is_obsolete: true + +[Term] +id: MS:1000621 +name: photodiode array detector +def: "An array detector used to record spectra in the ultraviolet and visible region of light." [PSI:MS] +synonym: "PDA" EXACT [] +is_a: MS:1000345 ! array detector + +[Term] +id: MS:1000622 +name: Surveyor PDA +def: "Surveyor PDA." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000623 +name: Accela PDA +def: "Accela PDA." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000624 +name: inductive detector +def: "Inductive detector." [PSI:MS] +synonym: "image current detector" EXACT [] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1000625 +name: chromatogram +def: "Representation of a chromatographic separation attribute measurement versus time." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000626 +name: chromatogram type +def: "Type of chromatogram measurement being represented." [PSI:MS] +relationship: part_of MS:1000625 ! chromatogram + +[Term] +id: MS:1000627 +name: selected ion current chromatogram +def: "Representation of an array of the measurements of a specific single ion current versus time." [PSI:MS] +synonym: "SIC chromatogram" EXACT [] +is_a: MS:1000810 ! ion current chromatogram + +[Term] +id: MS:1000628 +name: basepeak chromatogram +def: "Representation of an array of the most intense peaks versus time." [PSI:MS] +is_a: MS:1000810 ! ion current chromatogram + +[Term] +id: MS:1000629 +name: low intensity threshold +def: "Threshold below which some action is taken." [PSI:MS] +is_a: MS:1000630 ! data processing parameter +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 +relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000630 +name: data processing parameter +def: "Data processing parameter used in the data processing performed on the data file." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000631 +name: high intensity threshold +def: "Threshold above which some action is taken." [PSI:MS] +is_a: MS:1000630 ! data processing parameter +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 +relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000632 +name: Q-Tof Premier +def: "Waters oa-ToF based Q-Tof Premier." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1000633 +name: possible charge state +def: "A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1000634 +name: DSQ +def: "ThermoFinnigan DSQ GC-MS." [PSI:MS] +is_a: MS:1000125 ! Thermo Finnigan instrument model + +[Term] +id: MS:1000635 +name: ITQ 700 +def: "Thermo Scientific ITQ 700 GC-MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000636 +name: ITQ 900 +def: "Thermo Scientific ITQ 900 GC-MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000637 +name: ITQ 1100 +def: "Thermo Scientific ITQ 1100 GC-MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000638 +name: LTQ XL ETD +def: "Thermo Scientific LTQ XL MS with ETD." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000639 +name: LTQ Orbitrap XL ETD +def: "Thermo Scientific LTQ Orbitrap XL MS with ETD." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000640 +name: DFS +def: "Thermo Scientific DFS HR GC-MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000641 +name: DSQ II +def: "Thermo Scientific DSQ II GC-MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000642 +name: MALDI LTQ XL +def: "Thermo Scientific MALDI LTQ XL MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000643 +name: MALDI LTQ Orbitrap +def: "Thermo Scientific MALDI LTQ Orbitrap MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000644 +name: TSQ Quantum Access +def: "Thermo Scientific TSQ Quantum Access MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000645 +name: Element XR +def: "Thermo Scientific Element XR HR-ICP-MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000646 +name: Element 2 +def: "Thermo Scientific Element 2 HR-ICP-MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000647 +name: Element GD +def: "Thermo Scientific Element GD Glow Discharge MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000648 +name: GC IsoLink +def: "Thermo Scientific GC IsoLink Isotope Ratio MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000649 +name: Exactive +def: "Thermo Scientific Exactive MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000650 +name: Proteome Discoverer +def: "Thermo Scientific software for data analysis of peptides and proteins." [PSI:MS] +is_a: MS:1000693 ! Thermo Finnigan software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000651 +name: 3200 QTRAP +def: "SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000652 +name: 4800 Plus MALDI TOF/TOF +def: "SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000653 +name: API 3200 +def: "SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000654 +name: API 5000 +def: "SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000655 +name: QSTAR Elite +def: "SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000656 +name: QSTAR Pulsar +def: "Applied Biosystems|MDS SCIEX QSTAR Pulsar." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000657 +name: QSTAR XL +def: "Applied Biosystems|MDS SCIEX QSTAR XL." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000658 +name: 4800 Proteomics Analyzer +def: "Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer." [PSI:MS] +is_a: MS:1000495 ! Applied Biosystems instrument model + +[Term] +id: MS:1000659 +name: 4000 Series Explorer Software +def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000661 +name: GPS Explorer +def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000662 +name: LightSight Software +def: "SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000663 +name: ProteinPilot Software +def: "SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000664 +name: TissueView Software +def: "Applied Biosystems|MDS SCIEX software for tissue imaging." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000665 +name: MarkerView Software +def: "Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000666 +name: MRMPilot Software +def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000667 +name: BioAnalyst +def: "Applied Biosystems|MDS SCIEX software for bio-related data exploration." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000668 +name: Pro ID +def: "Applied Biosystems|MDS SCIEX software for protein identification." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000669 +name: Pro ICAT +def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000670 +name: Pro Quant +def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000671 +name: Pro BLAST +def: "Applied Biosystems|MDS SCIEX software for MS-BLAST identification." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000672 +name: Cliquid +def: "SCIEX Cliquid software for data analysis and quantitation." [PSI:MS] +is_a: MS:1000690 ! SCIEX software + +[Term] +id: MS:1000673 +name: MIDAS Workflow Designer +def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS] +is_a: MS:1000690 ! SCIEX software + +[Term] +id: MS:1000674 +name: MultiQuant +def: "Applied Biosystems|MDS SCIEX software for MRM-based quantitation." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000675 +name: 6220 Time-of-Flight LC/MS +def: "The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000676 +name: 6510 Quadrupole Time-of-Flight LC/MS +def: "The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000677 +name: 6520A Quadrupole Time-of-Flight LC/MS +def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000678 +name: MassHunter Data Acquisition +def: "Software for data acquisition of 6000 series instruments." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000679 +name: MassHunter Easy Access +def: "Software for open access data acquisition." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000680 +name: MassHunter Qualitative Analysis +def: "Software for data analysis of data from 6000 series instruments." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000681 +name: MassHunter Quantitative Analysis +def: "Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000682 +name: MassHunter Metabolite ID +def: "Software for identification of metabolites." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000683 +name: MassHunter BioConfirm +def: "Software for protein characterization." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000684 +name: Genespring MS +def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000685 +name: MassHunter Mass Profiler +def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000686 +name: METLIN +def: "Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000687 +name: Spectrum Mill for MassHunter Workstation +def: "Software for protein identification and characterization of complex protein digest mixtures." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000688 +name: 6300 Series Ion Trap Data Analysis Software +def: "Software for data analysis of 6300 series ion trap mass spectrometers." [PSI:MS] +is_a: MS:1000689 ! Agilent software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000689 +name: Agilent software +def: "Agilent software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1000690 +name: SCIEX software +def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1000691 +name: Applied Biosystems software +def: "Applied Biosystems|MDS SCIEX software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1000692 +name: Bruker software +def: "Bruker software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1000693 +name: Thermo Finnigan software +def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] +synonym: "Bioworks Browser" RELATED [] +is_a: MS:1000531 ! software + +[Term] +id: MS:1000694 +name: Waters software +def: "Waters software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1000695 +name: apex ultra +def: "Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] +is_a: MS:1001556 ! Bruker Daltonics apex series + +[Term] +id: MS:1000696 +name: autoflex III smartbeam +def: "Bruker Daltonics' autoflex III smartbeam: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000697 +name: Bruker Daltonics HCT Series +def: "Bruker Daltonics' HCT Series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1000698 +name: HCTultra +def: "Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1000697 ! Bruker Daltonics HCT Series + +[Term] +id: MS:1000699 +name: HCTultra PTM +def: "Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR." [PSI:MS] +is_a: MS:1000697 ! Bruker Daltonics HCT Series + +[Term] +id: MS:1000700 +name: HCTultra ETD II +def: "Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD." [PSI:MS] +is_a: MS:1000697 ! Bruker Daltonics HCT Series + +[Term] +id: MS:1000701 +name: microflex LT +def: "Bruker Daltonics' microflex LT: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000702 +name: micrOTOF +def: "Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1000703 +name: micrOTOF-Q +def: "Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1000704 +name: micrOTOF-Q II +def: "Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1000705 +name: ultraflex III TOF/TOF +def: "Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1000706 +name: apexControl +def: "Bruker software for data acquisition." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000707 +name: BioTools +def: "Bruker software for data analysis." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000708 +name: CLINPROT +def: "Bruker CLINPROT software." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000709 +name: CLINPROT micro +def: "Bruker CLINPROT micro software." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000710 +name: CLINPROT robot +def: "Bruker CLINPROT robot software." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000711 +name: ClinProTools +def: "Bruker ClinProTools software." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000712 +name: Compass +def: "Bruker Compass software." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000713 +name: Compass for HCT/esquire +def: "Bruker Compass for HCT/esquire software." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000714 +name: Compass for micrOTOF +def: "Bruker Compass for micrOTOF software." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000715 +name: Compass OpenAccess +def: "Bruker compass OpenAccess software." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000716 +name: Compass Security Pack +def: "Bruker compass Security Pack software." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000717 +name: CompassXport +def: "Bruker stand-alone software for data conversion." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000718 +name: CompassXtract +def: "Bruker software library for data access." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000719 +name: DataAnalysis +def: "Bruker software for data analysis." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000720 +name: dpControl +def: "Bruker software for data acquisition." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000721 +name: esquireControl +def: "Bruker software for data acquisition." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000722 +name: flexImaging +def: "Bruker software for data analysis." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000723 +name: GENOLINK +def: "Bruker GENOLINK software." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000724 +name: GenoTools +def: "Bruker GenoTools software." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000725 +name: HCTcontrol +def: "Bruker software for data acquisition." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000726 +name: micrOTOFcontrol +def: "Bruker software for data acquisition." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000727 +name: PolyTools +def: "Bruker PolyTools software." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000728 +name: ProfileAnalysis +def: "Bruker software for data analysis." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000729 +name: PROTEINEER +def: "Bruker PROTEINEER software." [PSI:PI] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000730 +name: PROTEINEER dp +def: "Bruker PROTEINEER dp software." [PSI:PI] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000731 +name: PROTEINEER fc +def: "Bruker PROTEINEER fc software." [PSI:PI] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000732 +name: PROTEINEER spII +def: "Bruker PROTEINEER spII software." [PSI:PI] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000733 +name: PROTEINEER-LC +def: "Bruker PROTEINEER-LC software." [PSI:PI] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000734 +name: ProteinScape +def: "Bruker ProteinScape software." [PSI:PI] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1000735 +name: PureDisk +def: "BrukerPureDisk software." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000736 +name: QuantAnalysis +def: "Bruker software for data analysis." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000737 +name: spControl +def: "Bruker software for data acquisition." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001455 ! acquisition software + +[Term] +id: MS:1000738 +name: TargetAnalysis +def: "Bruker TargetAnalysis software." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000739 +name: WARP-LC +def: "Bruker WARP-LC software." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1000740 +name: parameter file +def: "Parameter file used to configure the acquisition of raw data on the instrument." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000741 +name: Conversion to dta +def: "Conversion to dta format." [PSI:MS] +is_a: MS:1000530 ! file format conversion + +[Term] +id: MS:1000742 +name: Bioworks SRF format +def: "Thermo Finnigan SRF file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1000743 +name: TSQ Quantum Ultra AM +def: "Thermo Scientific TSQ Quantum Ultra AM." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000744 +name: selected ion m/z +def: "Mass-to-charge ratio of an selected ion." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000745 +name: retention time alignment +def: "The correction of the spectrum scan times, as used e.g. in label-free proteomics." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1000746 +name: high intensity data point removal +def: "The removal of very high intensity data points." [PSI:MS] +is_a: MS:1001486 ! data filtering + +[Term] +id: MS:1000747 +name: completion time +def: "The time that a data processing action was finished." [PSI:MS] +is_a: MS:1000630 ! data processing parameter +relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term + +[Term] +id: MS:1000748 +name: SSQ 7000 +def: "ThermoFinnigan SSQ 7000 MS." [PSI:MS] +is_a: MS:1000493 ! Finnigan MAT instrument model + +[Term] +id: MS:1000749 +name: TSQ 7000 +def: "ThermoFinnigan TSQ 7000 MS." [PSI:MS] +is_a: MS:1000493 ! Finnigan MAT instrument model + +[Term] +id: MS:1000750 +name: TSQ +def: "ThermoFinnigan TSQ MS." [PSI:MS] +is_a: MS:1000493 ! Finnigan MAT instrument model + +[Term] +id: MS:1000751 +name: TSQ Quantum Ultra +def: "Thermo Scientific TSQ Quantum Ultra." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000752 +name: TOPP software +def: "TOPP (The OpenMS proteomics pipeline) software." [PSI:MS] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1000753 +name: BaselineFilter +def: "Removes the baseline from profile spectra using a top-hat filter." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000754 +name: DBExporter +def: "Exports data from an OpenMS database to a file." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000755 +name: DBImporter +def: "Imports data to an OpenMS database." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000756 +name: FileConverter +def: "Converts between different MS file formats." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000757 +name: FileFilter +def: "Extracts or manipulates portions of data from peak, feature or consensus feature files." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000758 +name: FileMerger +def: "Merges several MS files into one file." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000759 +name: InternalCalibration +def: "Applies an internal calibration." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000760 +name: MapAligner +def: "OBSOLETE Corrects retention time distortions between maps." [PSI:MS] +comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch. +is_a: MS:1000752 ! TOPP software +is_obsolete: true + +[Term] +id: MS:1000761 +name: MapNormalizer +def: "Normalizes peak intensities in an MS run." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000762 +name: NoiseFilter +def: "OBSOLETE Removes noise from profile spectra by using different smoothing techniques." [PSI:MS] +comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch. +is_a: MS:1000752 ! TOPP software +is_obsolete: true + +[Term] +id: MS:1000763 +name: PeakPicker +def: "OBSOLETE Finds mass spectrometric peaks in profile mass spectra." [PSI:MS] +comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch. +is_a: MS:1000752 ! TOPP software +is_obsolete: true + +[Term] +id: MS:1000764 +name: Resampler +def: "Transforms an LC/MS map into a resampled map or a png image." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000765 +name: SpectraFilter +def: "OBSOLETE Applies a filter to peak spectra." [PSI:MS] +comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch. +is_a: MS:1000752 ! TOPP software +is_obsolete: true + +[Term] +id: MS:1000766 +name: TOFCalibration +def: "Applies time of flight calibration." [PSI:MS] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1000767 +name: native spectrum identifier format +def: "Describes how the native spectrum identifiers are formated." [PSI:MS] +synonym: "nativeID format" EXACT [] +relationship: part_of MS:1000577 ! source data file + +[Term] +id: MS:1000768 +name: Thermo nativeID format +def: "Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000769 +name: Waters nativeID format +def: "Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000770 +name: WIFF nativeID format +def: "Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000771 +name: Bruker/Agilent YEP nativeID format +def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000772 +name: Bruker BAF nativeID format +def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000773 +name: Bruker FID nativeID format +def: "Native format defined by file=xsd:IDREF." [PSI:MS] +comment: The nativeID must be the same as the source file ID. +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000774 +name: multiple peak list nativeID format +def: "Native format defined by index=xsd:nonNegativeInteger." [PSI:MS] +comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000775 +name: single peak list nativeID format +def: "Native format defined by file=xsd:IDREF." [PSI:MS] +comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000776 +name: scan number only nativeID format +def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] +comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000777 +name: spectrum identifier nativeID format +def: "Native format defined by spectrum=xsd:nonNegativeInteger." [PSI:MS] +comment: Used for conversion from mzData. The spectrum id attribute is referenced. +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000778 +name: charge state calculation +def: "A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1000779 +name: below precursor intensity dominance charge state calculation +def: "Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z." [PSI:MS] +is_a: MS:1000778 ! charge state calculation + +[Term] +id: MS:1000780 +name: precursor recalculation +def: "A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1000781 +name: msPrefix precursor recalculation +def: "Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans." [PSI:MS] +is_a: MS:1000780 ! precursor recalculation + +[Term] +id: MS:1000782 +name: Savitzky-Golay smoothing +def: "Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques." [PSI:MS] +is_a: MS:1000592 ! smoothing + +[Term] +id: MS:1000783 +name: LOWESS smoothing +def: "Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible." [PSI:MS] +is_a: MS:1000592 ! smoothing + +[Term] +id: MS:1000784 +name: Gaussian smoothing +def: "Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function." [PSI:MS] +synonym: "binomial smoothing" EXACT [] +synonym: "Weierstrass transform" EXACT [] +is_a: MS:1000592 ! smoothing + +[Term] +id: MS:1000785 +name: moving average smoothing +def: "Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect." [PSI:MS] +synonym: "box smoothing" EXACT [] +synonym: "boxcar smoothing" EXACT [] +synonym: "sliding average smoothing" EXACT [] +is_a: MS:1000592 ! smoothing + +[Term] +id: MS:1000786 +name: non-standard data array +def: "A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added." [PSI:MS] +xref: binary-data-type:MS\:1000519 "32-bit integer" +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000522 "64-bit integer" +xref: binary-data-type:MS\:1000523 "64-bit float" +xref: binary-data-type:MS\:1001479 "null-terminated ASCII string" +is_a: MS:1000513 ! binary data array +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000787 +name: inclusive low intensity threshold +def: "Threshold at or below which some action is taken." [PSI:MS] +is_a: MS:1000630 ! data processing parameter +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 +relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000788 +name: inclusive high intensity threshold +def: "Threshold at or above which some action is taken." [PSI:MS] +is_a: MS:1000630 ! data processing parameter +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 +relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000789 +name: enhanced multiply charged spectrum +def: "MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions." [PSI:MS] +is_a: MS:1000579 ! MS1 spectrum + +[Term] +id: MS:1000790 +name: time-delayed fragmentation spectrum +def: "MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation." [PSI:MS] +is_a: MS:1000580 ! MSn spectrum + +[Term] +id: MS:1000791 +name: enhanced resolution scan +def: "OBSOLETE Scan with enhanced resolution." [PSI:MS] +comment: This term was made obsolete because it was merged with zoom scan (MS:1000497). +is_obsolete: true + +[Term] +id: MS:1000792 +name: isolation window attribute +def: "Isolation window parameter." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000441 ! scan + +[Term] +id: MS:1000793 +name: isolation window upper limit +def: "OBSOLETE The highest m/z being isolated in an isolation window." [PSI:MS] +comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. +is_a: MS:1000792 ! isolation window attribute +relationship: has_units MS:1000040 ! m/z +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000794 +name: isolation window lower limit +def: "OBSOLETE The lowest m/z being isolated in an isolation window." [PSI:MS] +comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. +is_a: MS:1000792 ! isolation window attribute +relationship: has_units MS:1000040 ! m/z +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000795 +name: no combination +def: "Use this term if only one scan was recorded or there is no information about scans available." [PSI:MS] +is_a: MS:1000570 ! spectra combination + +[Term] +id: MS:1000796 +name: spectrum title +def: "Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file." [PSI:MS] +comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list. +is_a: MS:1001405 ! spectrum identification result details +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000797 +name: peak list scans +def: "A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS] +comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list. +is_a: MS:1001405 ! spectrum identification result details +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000798 +name: peak list raw scans +def: "A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS] +comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list. +is_a: MS:1001405 ! spectrum identification result details +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000799 +name: custom unreleased software tool +def: "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added." [PSI:MS] +is_a: MS:1000531 ! software +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000800 +name: mass resolving power +def: "The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000801 +name: area peak picking +def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported." [PSI:MS] +synonym: "sum peak picking" EXACT [] +is_a: MS:1000035 ! peak picking + +[Term] +id: MS:1000802 +name: height peak picking +def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported." [PSI:MS] +synonym: "max peak picking" EXACT [] +is_a: MS:1000035 ! peak picking + +[Term] +id: MS:1000803 +name: analyzer scan offset +def: "Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000804 +name: electromagnetic radiation spectrum +def: "A plot of the relative intensity of electromagnetic radiation as a function of the wavelength." [PSI:MS] +synonym: "EMR spectrum" EXACT [] +is_a: MS:1000524 ! data file content +is_a: MS:1000559 ! spectrum type + +[Term] +id: MS:1000805 +name: emission spectrum +def: "A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited." [PSI:MS] +is_a: MS:1000524 ! data file content +is_a: MS:1000559 ! spectrum type + +[Term] +id: MS:1000806 +name: absorption spectrum +def: "A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited." [PSI:MS] +is_a: MS:1000524 ! data file content +is_a: MS:1000559 ! spectrum type + +[Term] +id: MS:1000807 +name: Th/s +def: "Unit describing the scan rate of a spectrum in Thomson per second." [PSI:MS] +is_a: UO:0000000 ! unit + +[Term] +id: MS:1000808 +name: chromatogram attribute +def: "Chromatogram properties that are associated with a value." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000625 ! chromatogram + +[Term] +id: MS:1000809 +name: chromatogram title +def: "A free-form text title describing a chromatogram." [PSI:MS] +comment: This is the preferred storage place for the spectrum title. +is_a: MS:1000808 ! chromatogram attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000810 +name: ion current chromatogram +def: "Representation of the current of ions versus time." [PSI:MS] +is_a: MS:1000524 ! data file content +is_a: MS:1000626 ! chromatogram type + +[Term] +id: MS:1000811 +name: electromagnetic radiation chromatogram +def: "Representation of electromagnetic properties versus time." [PSI:MS] +synonym: "EMR radiation chromatogram" EXACT [] +is_a: MS:1000524 ! data file content +is_a: MS:1000626 ! chromatogram type + +[Term] +id: MS:1000812 +name: absorption chromatogram +def: "Representation of light absorbed by the sample versus time." [PSI:MS] +is_a: MS:1000811 ! electromagnetic radiation chromatogram + +[Term] +id: MS:1000813 +name: emission chromatogram +def: "Representation of light emitted by the sample versus time." [PSI:MS] +is_a: MS:1000811 ! electromagnetic radiation chromatogram + +[Term] +id: MS:1000814 +name: counts per second +def: "The number of counted events observed per second in one or a group of elements of a detector." [PSI:MS] +is_a: MS:1000043 ! intensity unit + +[Term] +id: MS:1000815 +name: Bruker BAF format +def: "Bruker BAF raw file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000816 +name: Bruker U2 format +def: "Bruker HyStar U2 file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000817 +name: HyStar +def: "Bruker software for hyphenated experiments." [PSI:MS] +is_a: MS:1000692 ! Bruker software + +[Term] +id: MS:1000818 +name: Acquity UPLC PDA +def: "Acquity UPLC Photodiode Array Detector." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model +is_a: MS:1000621 ! photodiode array detector + +[Term] +id: MS:1000819 +name: Acquity UPLC FLR +def: "Acquity UPLC Fluorescence Detector." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model +is_a: MS:1002308 ! fluorescence detector + +[Term] +id: MS:1000820 +name: flow rate array +def: "A data array of flow rate measurements." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units UO:0000271 ! microliters per minute + +[Term] +id: MS:1000821 +name: pressure array +def: "A data array of pressure measurements." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units UO:0000110 ! pascal + +[Term] +id: MS:1000822 +name: temperature array +def: "A data array of temperature measurements." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units UO:0000012 ! kelvin + +[Term] +id: MS:1000823 +name: Bruker U2 nativeID format +def: "Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000824 +name: no nativeID format +def: "No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000825 +name: Bruker FID format +def: "Bruker FID file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000826 +name: elution time +def: "The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000827 +name: isolation window target m/z +def: "The primary or reference m/z about which the isolation window is defined." [PSI:MS] +is_a: MS:1000792 ! isolation window attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000828 +name: isolation window lower offset +def: "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] +is_a: MS:1000792 ! isolation window attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000829 +name: isolation window upper offset +def: "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] +is_a: MS:1000792 ! isolation window attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000831 +name: sample preparation +def: "Properties of the preparation steps which took place before the measurement was performed." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000548 ! sample attribute + +[Term] +id: MS:1000832 +name: MALDI matrix application +def: "Attributes to describe the technique how the sample is prepared with the matrix solution." [PSI:MS] +relationship: part_of MS:1000831 ! sample preparation + +[Term] +id: MS:1000833 +name: matrix application type +def: "Describes the technique how the matrix is put on the sample target." [PSI:MS] +relationship: part_of MS:1000832 ! MALDI matrix application + +[Term] +id: MS:1000834 +name: matrix solution +def: "Describes the chemical solution used as matrix." [PSI:MS] +is_a: MS:1000832 ! MALDI matrix application +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000835 +name: matrix solution concentration +def: "Concentration of the chemical solution used as matrix." [PSI:MS] +is_a: MS:1000832 ! MALDI matrix application +relationship: has_units UO:0000175 ! gram per liter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000836 +name: dried droplet MALDI matrix preparation +def: "Dried droplet in MALDI matrix preparation." [PSI:MS] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1000837 +name: printed MALDI matrix preparation +def: "Printed MALDI matrix preparation." [PSI:MS] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1000838 +name: sprayed MALDI matrix preparation +def: "Sprayed MALDI matrix preparation." [PSI:MS] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1000839 +name: precoated MALDI sample plate +def: "Precoated MALDI sample plate." [PSI:MS] +is_a: MS:1000833 ! matrix application type +is_a: MS:1001938 ! sample plate type + +[Term] +id: MS:1000840 +name: laser +def: "Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation." [PSI:MS] +relationship: part_of MS:1000482 ! source attribute + +[Term] +id: MS:1000841 +name: laser attribute +def: "Laser properties that are associated with a value." [PSI:MS] +relationship: part_of MS:1000840 ! laser + +[Term] +id: MS:1000842 +name: laser type +def: "Type of laser used for desorption purpose." [PSI:MS] +relationship: part_of MS:1000840 ! laser + +[Term] +id: MS:1000843 +name: wavelength +def: "OBSOLETE The distance between two peaks of the emitted laser beam." [PSI:MS] +comment: This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242). +is_a: MS:1000841 ! laser attribute +relationship: has_units UO:0000018 ! nanometer +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000844 +name: focus diameter x +def: "Describes the diameter of the laser beam in x direction." [PSI:MS] +is_a: MS:1000841 ! laser attribute +relationship: has_units UO:0000017 ! micrometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000845 +name: focus diameter y +def: "Describes the diameter of the laser beam in y direction." [PSI:MS] +is_a: MS:1000841 ! laser attribute +relationship: has_units UO:0000017 ! micrometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000846 +name: pulse energy +def: "Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS] +is_a: MS:1000841 ! laser attribute +relationship: has_units UO:0000112 ! joule +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000847 +name: pulse duration +def: "Describes how long the laser beam was emitted from the laser device." [PSI:MS] +is_a: MS:1000841 ! laser attribute +relationship: has_units UO:0000150 ! nanosecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000848 +name: attenuation +def: "Describes the reduction of the intensity of the laser beam energy." [PSI:MS] +is_a: MS:1000841 ! laser attribute +relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000849 +name: impact angle +def: "Describes the angle between the laser beam and the sample target." [PSI:MS] +is_a: MS:1000841 ! laser attribute +relationship: has_units UO:0000185 ! degree +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000850 +name: gas laser +def: "Laser which is powered by a gaseous medium." [PSI:MS] +is_a: MS:1000842 ! laser type + +[Term] +id: MS:1000851 +name: solid-state laser +def: "Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states." [PSI:MS] +is_a: MS:1000842 ! laser type + +[Term] +id: MS:1000852 +name: dye-laser +def: "Dye lasers use an organic dye as the gain medium." [PSI:MS] +is_a: MS:1000842 ! laser type + +[Term] +id: MS:1000853 +name: free electron laser +def: "Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term." [PSI:MS] +is_a: MS:1000842 ! laser type + +[Term] +id: MS:1000854 +name: LTQ XL +def: "Thermo Scientific LTQ XL MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000855 +name: LTQ Velos +def: "Thermo Scientific LTQ Velos MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000856 +name: LTQ Velos ETD +def: "Thermo Scientific LTQ Velos MS with ETD." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1000857 +name: run attribute +def: "Properties of the described run." [PSI:MS] +is_a: MS:1000547 ! object attribute + +[Term] +id: MS:1000858 +name: fraction identifier +def: "Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information." [PSI:MS] +is_a: MS:1000857 ! run attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000859 +name: molecule +def: "Group of two or more atoms held together by chemical bonds." [https://en.wikipedia.org/wiki/Molecule] +is_a: MS:1000881 ! molecular entity + +[Term] +id: MS:1000860 +name: peptide +def: "A molecule of low molecular weight that is composed of two or more amino acid residues." [PSI:MS] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1000861 +name: molecular entity property +def: "A physical characteristic of a molecular entity." [PSI:MS] +relationship: part_of MS:1000881 ! molecular entity + +[Term] +id: MS:1000862 +name: isoelectric point +def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS] +synonym: "pI" EXACT [] +is_a: MS:1000861 ! molecular entity property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000863 +name: predicted isoelectric point +def: "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS] +synonym: "predicted pI" EXACT [] +is_a: MS:1000862 ! isoelectric point +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000864 +name: chemical formula +def: "A combination of symbols used to express the chemical composition of a molecule." [EDAM:0846] +is_a: MS:1003033 ! molecular entity attribute + +[Term] +id: MS:1000865 +name: empirical formula +def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS] +is_a: MS:1000864 ! chemical formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000866 +name: molecular formula +def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS] +is_a: MS:1000864 ! chemical formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000867 +name: structural formula +def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS] +is_a: MS:1000864 ! chemical formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000868 +name: SMILES formula +def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301] +is_a: MS:1000864 ! chemical formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000869 +name: collision gas pressure +def: "The gas pressure of the collision gas used for collisional excitation." [PSI:MS] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_units UO:0000110 ! pascal +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000870 +name: 4000 QTRAP +def: "OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000." [PSI:MS] +comment: This term was obsoleted because was redundant to MS:1000139. +is_a: MS:1000121 ! SCIEX instrument model +is_obsolete: true + +[Term] +id: MS:1000871 +name: SRM software +def: "Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1000872 +name: MaRiMba +def: "Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba] +is_a: MS:1000871 ! SRM software + +[Term] +id: MS:1000873 +name: peptide attribute calculation software +def: "Software used to predict or calculate numerical attributes of peptides." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1000874 +name: SSRCalc +def: "Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence." [http://hs2.proteome.ca/SSRCalc/SSRCalc.html] +is_a: MS:1000873 ! peptide attribute calculation software + +[Term] +id: MS:1000875 +name: declustering potential +def: "Potential difference between the orifice and the skimmer in volts." [PSI:MS] +is_a: MS:1000482 ! source attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000876 +name: cone voltage +def: "Potential difference between the sampling cone/orifice in volts." [PSI:MS] +is_a: MS:1000482 ! source attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000877 +name: tube lens voltage +def: "Potential difference setting of the tube lens in volts." [PSI:MS] +is_a: MS:1000482 ! source attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000878 +name: external reference identifier +def: "An identifier/accession number to an external reference database." [PSI:MS] +is_a: MS:1002840 ! external reference data + +[Term] +id: MS:1000879 +name: PubMed identifier +def: "A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1000880 +name: interchannel delay +def: "The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000881 +name: molecular entity +def: "Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [https://en.wikipedia.org/wiki/Molecular_entity] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1000882 +name: protein +def: "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene." [PSI:MS] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1000883 +name: protein short name +def: "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN)." [PSI:MS] +is_a: MS:1000884 ! protein attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000884 +name: protein attribute +def: "An nonphysical characterstic attributed to a specific protein." [PSI:MS] +relationship: part_of MS:1000882 ! protein +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1000885 +name: protein accession +def: "Identifier for a specific protein in a database." [PSI:MS] +is_a: MS:1000884 ! protein attribute +is_a: MS:1003046 ! peptide-to-protein mapping attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000886 +name: protein name +def: "A long name describing the function of the protein." [PSI:MS] +is_a: MS:1000884 ! protein attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000887 +name: peptide attribute +def: "Nonphysical characteristic attributed to a peptide." [PSI:MS] +relationship: part_of MS:1000860 ! peptide + +[Term] +id: MS:1000888 +name: stripped peptide sequence +def: "Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away." [PSI:MS] +is_a: MS:1003050 ! peptidoform attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000889 +name: peptidoform sequence +def: "Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present." [PSI:MS] +comment: Make it more general as there are actually many other ways to display a modified peptide sequence. +is_a: MS:1003050 ! peptidoform attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000890 +name: peptidoform labeling state +def: "A state description of how a peptide might be isotopically or isobarically labelled." [PSI:MS] +is_a: MS:1003050 ! peptidoform attribute + +[Term] +id: MS:1000891 +name: heavy labeled peptidoform +def: "A peptide that has been created or labelled with some heavier-than-usual isotopes." [PSI:MS] +is_a: MS:1000890 ! peptidoform labeling state + +[Term] +id: MS:1000892 +name: unlabeled peptidoform +def: "A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:MS] +synonym: "light labeled peptide" EXACT [] +is_a: MS:1000890 ! peptidoform labeling state + +[Term] +id: MS:1000893 +name: peptidoform group label +def: "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS] +is_a: MS:1003050 ! peptidoform attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000894 +name: retention time +def: "A time interval from the start of chromatography when an analyte exits a chromatographic column." [PSI:MS] +is_a: MS:1003050 ! peptidoform attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000895 +name: local retention time +def: "A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup." [PSI:MS] +is_a: MS:1000894 ! retention time +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000896 +name: normalized retention time +def: "A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup." [PSI:MS] +is_a: MS:1000894 ! retention time +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000897 +name: predicted retention time +def: "A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application." [PSI:MS] +is_a: MS:1000894 ! retention time +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000898 +name: standard +def: "Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1000899 +name: de facto standard +def: "A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard." [PSI:MS] +is_a: MS:1000898 ! standard + +[Term] +id: MS:1000900 +name: minimum information standard +def: "A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result." [PSI:MS] +is_a: MS:1000898 ! standard + +[Term] +id: MS:1000901 +name: retention time normalization standard +def: "A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column." [PSI:MS] +is_a: MS:1000898 ! standard + +[Term] +id: MS:1000902 +name: H-PINS retention time normalization standard +def: "The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column." [DOI:10.1074/mcp.M800569-MCP200, PMID:19411281] +is_a: MS:1000901 ! retention time normalization standard + +[Term] +id: MS:1000903 +name: product ion series ordinal +def: "The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion)." [PSI:PI] +is_a: MS:1001221 ! product ion attribute +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1000904 +name: product ion m/z delta +def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI] +is_a: MS:1001221 ! product ion attribute +relationship: has_units MS:1000040 ! m/z + +[Term] +id: MS:1000905 +name: percent of base peak times 100 +def: "The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries." [PSI:MS] +is_a: MS:1000043 ! intensity unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000906 +name: peak intensity rank +def: "Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +relationship: part_of MS:1000231 ! peak +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1000907 +name: peak targeting suitability rank +def: "Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +relationship: part_of MS:1000231 ! peak +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1000908 +name: transition +def: "A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely." [PSI:MS] +synonym: "reaction" EXACT [] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000909 +name: transition validation method +def: "The strategy used to validate that a transition is effective." [PSI:MS] +relationship: part_of MS:1000908 ! transition + +[Term] +id: MS:1000910 +name: transition optimized on specified instrument +def: "The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined." [PSI:MS] +is_a: MS:1000909 ! transition validation method + +[Term] +id: MS:1000911 +name: transition validated with an MS/MS spectrum on specified instrument +def: "The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term." [PSI:MS] +is_a: MS:1000909 ! transition validation method + +[Term] +id: MS:1000912 +name: transition purported from an MS/MS spectrum on a different, specified instrument +def: "The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad)." [PSI:MS] +is_a: MS:1000909 ! transition validation method + +[Term] +id: MS:1000913 +name: transition predicted by informatic analysis +def: "The transition has been predicted by informatics software without any direct spectral evidence." [PSI:MS] +is_a: MS:1000909 ! transition validation method + +[Term] +id: MS:1000914 +name: tab delimited text format +def: "A file format that has two or more columns of tabular data where each column is separated by a TAB character." [PSI:MS] +is_a: MS:1001459 ! file format +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1000915 +name: retention time window attribute +def: "An attribute of a window in time about which a peptide might elute from the column." [PSI:MS] +relationship: part_of MS:1000894 ! retention time + +[Term] +id: MS:1000916 +name: retention time window lower offset +def: "The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS] +is_a: MS:1000915 ! retention time window attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000917 +name: retention time window upper offset +def: "The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS] +is_a: MS:1000915 ! retention time window attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000918 +name: target list +def: "A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information + +[Term] +id: MS:1000919 +name: target inclusion exclusion priority +def: "A priority setting specifying whether included or excluded targets have priority over the other." [PSI:MS] +relationship: part_of MS:1000918 ! target list + +[Term] +id: MS:1000920 +name: includes supersede excludes +def: "A priority setting specifying that included targets have priority over the excluded targets if there is a conflict." [PSI:MS] +is_a: MS:1000919 ! target inclusion exclusion priority + +[Term] +id: MS:1000921 +name: excludes supersede includes +def: "A priority setting specifying that excluded targets have priority over the included targets if there is a conflict." [PSI:MS] +is_a: MS:1000919 ! target inclusion exclusion priority + +[Term] +id: MS:1000922 +name: Skyline +def: "Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington." [https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default] +is_a: MS:1000871 ! SRM software +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1000923 +name: TIQAM +def: "Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/TIQAM/TIQAM.html] +is_a: MS:1000871 ! SRM software + +[Term] +id: MS:1000924 +name: MaRiMba +def: "OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba] +comment: This term was made obsolete because it was redundant with an existing term (MS:1000872). +is_obsolete: true +replaced_by: MS:1000872 + +[Term] +id: MS:1000925 +name: ATAQS +def: "Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology." [PSI:MS] +is_a: MS:1000871 ! SRM software + +[Term] +id: MS:1000926 +name: product interpretation rank +def: "The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1." [PSI:MS] +is_a: MS:1001221 ! product ion attribute +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1000927 +name: ion injection time +def: "The length of time spent filling an ion trapping device." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000928 +name: calibration spectrum +def: "A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample." [PSI:MS] +is_a: MS:1000559 ! spectrum type + +[Term] +id: MS:1000929 +name: Shimadzu Biotech nativeID format +def: "Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1000930 +name: Shimadzu Biotech database entity +def: "Shimadzu Biotech format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1000931 +name: QTRAP 5500 +def: "Applied Biosystems|MDS SCIEX QTRAP 5500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000932 +name: TripleTOF 5600 +def: "SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1000933 +name: protein modifications +def: "Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation." [PSI:MS] +is_a: MS:1000884 ! protein attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000934 +name: gene name +def: "Name of the gene from which the protein is translated." [PSI:MS] +is_a: MS:1000884 ! protein attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000935 +name: 6470A Triple Quadrupole LC/MS +def: "The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000936 +name: 6470B Triple Quadrupole LC/MS +def: "The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000937 +name: 6495C Triple Quadrupole LC/MS +def: "The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1001000 +name: spectrum interpretation +def: "Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra." [PSI:PI] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1001005 +name: SEQUEST:CleavesAt +is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001006 +name: SEQUEST:ViewCV +def: "SEQUEST View Input Parameters." [PSI:PI] +is_a: MS:1002096 ! SEQUEST input parameter + +[Term] +id: MS:1001007 +name: SEQUEST:OutputLines +def: "Number of peptide results to show." [PSI:MS] +is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001009 +name: SEQUEST:DescriptionLines +def: "Number of full protein descriptions to show for top N peptides." [PSI:MS] +is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001010 +name: de novo search +def: "A de novo sequencing search (without database)." [PSI:PI] +is_a: MS:1001080 ! search type + +[Term] +id: MS:1001011 +name: search database details +def: "Details about the database searched." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001012 +name: database source +def: "The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other)." [PSI:PI] +is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001013 +name: database name +def: "The name of the search database (nr, SwissProt or est_human)." [PSI:PI] +is_a: MS:1001011 ! search database details + +[Term] +id: MS:1001014 +name: database local file path +def: "OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view." [PSI:PI] +is_a: MS:1001011 ! search database details +is_obsolete: true + +[Term] +id: MS:1001015 +name: database original uri +def: "URI, from where the search database was originally downloaded." [PSI:PI] +is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1001016 +name: database version +def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI] +is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001017 +name: release date +def: "Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term." [PSI:PI] +is_a: MS:1001011 ! search database details +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:dateTime +relationship: has_structured_representation_in_format MS:1002073 ! mzIdentML format + +[Term] +id: MS:1001018 +name: database type +def: "Database containing amino acid or nucleic acid sequences." [PSI:PI] +is_a: MS:1001011 ! search database details + +[Term] +id: MS:1001019 +name: database filtering +def: "Was there filtering used on the database." [PSI:PI] +is_a: MS:1001011 ! search database details + +[Term] +id: MS:1001020 +name: DB filter taxonomy +def: "A taxonomy filter was to the database search." [PSI:PI] +is_a: MS:1001511 ! Sequence database filter types + +[Term] +id: MS:1001021 +name: DB filter on accession numbers +def: "Filtering applied specifically by accession number pattern." [PSI:PI] +is_a: MS:1001511 ! Sequence database filter types + +[Term] +id: MS:1001022 +name: DB MW filter +def: "Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value." [PSI:PI] +is_a: MS:1001511 ! Sequence database filter types + +[Term] +id: MS:1001023 +name: DB PI filter +def: "Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value." [PSI:PI] +is_a: MS:1001511 ! Sequence database filter types + +[Term] +id: MS:1001024 +name: translation frame +def: "The translated open reading frames from a nucleotide database considered in the search (range: 1-6)." [PSI:PI] +is_a: MS:1001011 ! search database details + +[Term] +id: MS:1001025 +name: translation table +def: "The translation table used to translate the nucleotides to amino acids." [PSI:PI] +is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001026 +name: SEQUEST:NormalizeXCorrValues +is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001027 +name: DB filter on sequence pattern +def: "Filtering applied specifically by amino acid sequence pattern." [PSI:PI] +is_a: MS:1001511 ! Sequence database filter types + +[Term] +id: MS:1001028 +name: SEQUEST:SequenceHeaderFilter +def: "String in the header of a sequence entry for that entry to be searched." [PSI:MS] +is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001029 +name: number of sequences searched +def: "The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI] +is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001030 +name: number of peptide seqs compared to each spectrum +def: "Number of peptide seqs compared to each spectrum." [PSI:PI] +is_a: MS:1001011 ! search database details +is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001031 +name: spectral library search +def: "A search using a library of spectra." [PSI:PI] +is_a: MS:1001080 ! search type + +[Term] +id: MS:1001032 +name: SEQUEST:SequencePartialFilter +is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001035 +name: date / time search performed +def: "OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run." [PSI:PI] +is_a: MS:1001184 ! search statistics +is_obsolete: true + +[Term] +id: MS:1001036 +name: search time taken +def: "The time taken to complete the search in seconds." [PSI:PI] +is_a: MS:1001184 ! search statistics +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001037 +name: SEQUEST:ShowFragmentIons +def: "Flag indicating that fragment ions should be shown." [PSI:MS] +is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001038 +name: SEQUEST:Consensus +def: "Specify depth as value of the CVParam." [PSI:PI] +is_a: MS:1001006 ! SEQUEST:ViewCV +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001040 +name: intermediate analysis format +def: "Type of the source file, the mzIdentML was created from." [PSI:PI] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1001041 +name: SEQUEST:sortCV +def: "SEQUEST View / Sort Input Parameters." [PSI:PI] +is_a: MS:1001006 ! SEQUEST:ViewCV + +[Term] +id: MS:1001042 +name: SEQUEST:LimitTo +def: "Specify \"number of dtas shown\" as value of the CVParam." [PSI:PI] +is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001044 +name: cleavage agent details +def: "Details of cleavage agent (enzyme)." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001045 +name: cleavage agent name +def: "The name of the cleavage agent." [PSI:PI] +is_a: MS:1001044 ! cleavage agent details + +[Term] +id: MS:1001046 +name: SEQUEST:sort by dCn +def: "Sort order of SEQUEST search results by the delta of the normalized correlation score." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001047 +name: SEQUEST:sort by dM +def: "Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001048 +name: SEQUEST:sort by Ions +def: "Sort order of SEQUEST search results given by the ions." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001049 +name: SEQUEST:sort by MH+ +def: "Sort order of SEQUEST search results given by the mass of the protonated ion." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001050 +name: SEQUEST:sort by P +def: "Sort order of SEQUEST search results given by the probability." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001051 +name: multiple enzyme combination rules +def: "OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any." [PSI:PI] +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001052 +name: SEQUEST:sort by PreviousAminoAcid +def: "Sort order of SEQUEST search results given by the previous amino acid." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001053 +name: SEQUEST:sort by Ref +def: "Sort order of SEQUEST search results given by the reference." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001055 +name: modification parameters +def: "Modification parameters for the search engine run." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1001056 +name: modification specificity rule +def: "The specificity rules for the modifications applied by the search engine." [PSI:PI] +is_a: MS:1001055 ! modification parameters + +[Term] +id: MS:1001057 +name: tolerance on types +def: "OBSOLETE: Tolerance on types." [PSI:PI] +is_a: MS:1001055 ! modification parameters +is_obsolete: true + +[Term] +id: MS:1001058 +name: quality estimation by manual validation +def: "The quality estimation was done manually." [PSI:PI] +is_a: MS:1001060 ! quality estimation method details + +[Term] +id: MS:1001059 +name: SEQUEST:sort by RSp +def: "Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide)." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001060 +name: quality estimation method details +def: "Method for quality estimation (manually or with decoy database)." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001061 +name: neutral loss +def: "OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD." [PSI:PI] +is_a: MS:1001055 ! modification parameters +is_obsolete: true +replaced_by: MS:1000336 + +[Term] +id: MS:1001062 +name: Mascot MGF format +def: "Mascot MGF file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001065 +name: TODOscoring model +def: "OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms." [PSI:PI] +comment: This term was made obsolete and is replaced by the term (MS:1001961). +is_a: MS:1001249 ! search input details +is_obsolete: true +replaced_by: MS:1001961 + +[Term] +id: MS:1001066 +name: ions series considered in search +def: "The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001068 +name: SEQUEST:sort by Sp +def: "Sort order of SEQUEST search results by the Sp score." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001069 +name: SEQUEST:sort by TIC +def: "Sort order of SEQUEST search results given by the total ion current." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001070 +name: SEQUEST:sort by Scan +def: "Sort order of SEQUEST search results given by the scan number." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001071 +name: SEQUEST:sort by Sequence +def: "Sort order of SEQUEST search results given by the sequence." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001072 +name: SEQUEST:sort by Sf +def: "Sort order of SEQUEST search results given by the SEQUEST result 'Sf'." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001073 +name: database type amino acid +def: "Database contains amino acid sequences." [PSI:PI] +is_a: MS:1001018 ! database type + +[Term] +id: MS:1001079 +name: database type nucleotide +def: "Database contains nucleic acid sequences." [PSI:PI] +is_a: MS:1001018 ! database type + +[Term] +id: MS:1001080 +name: search type +def: "Enumeration of type of search value (i.e. from PMF, sequence tag, MS2)." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001081 +name: pmf search +def: "A peptide mass fingerprint search." [PSI:PI] +is_a: MS:1001080 ! search type + +[Term] +id: MS:1001082 +name: tag search +def: "A sequence tag search." [PSI:PI] +is_a: MS:1001080 ! search type + +[Term] +id: MS:1001083 +name: ms-ms search +def: "An MS2 search (with fragment ions)." [PSI:PI] +is_a: MS:1001080 ! search type + +[Term] +id: MS:1001084 +name: database nr +def: "Non-redundant GenBank sequence database." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1001085 +name: protein-level identification attribute +def: "Protein level information." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1001086 +name: SEQUEST:sort by XCorr +def: "Sort order of SEQUEST search results by the correlation score." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001087 +name: SEQUEST:ProcessCV +def: "SEQUEST View / Process Input Parameters." [PSI:PI] +is_a: MS:1002096 ! SEQUEST input parameter + +[Term] +id: MS:1001088 +name: protein description +def: "The protein description line from the sequence entry in the source database FASTA file." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +is_a: MS:1001342 ! database sequence details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001089 +name: molecule taxonomy +def: "The taxonomy of the resultant molecule from the search." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +is_a: MS:1001342 ! database sequence details +is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001090 +name: taxonomy nomenclature +def: "OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI] +is_a: MS:1001089 ! molecule taxonomy +is_obsolete: true +replaced_by: MS:1001467 +replaced_by: MS:1001468 +replaced_by: MS:1001469 +replaced_by: MS:1001470 + +[Term] +id: MS:1001091 +name: NoEnzyme +is_a: MS:1001045 ! cleavage agent name +comment: This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956). +is_obsolete: true + +[Term] +id: MS:1001092 +name: peptide sequence-level identification statistic +def: "Identification confidence metric for a peptide." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute + +[Term] +id: MS:1001093 +name: sequence coverage +def: "The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:decimal ! The allowed value-type for this CV term + +[Term] +id: MS:1001094 +name: SEQUEST:sort by z +def: "Sort order of SEQUEST search results given by the charge." [PSI:PI] +is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001095 +name: SEQUEST:ProcessAll +is_a: MS:1001087 ! SEQUEST:ProcessCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001096 +name: SEQUEST:TopPercentMostIntense +def: "Specify \"percentage\" as value of the CVParam." [PSI:PI] +is_a: MS:1001087 ! SEQUEST:ProcessCV +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001097 +name: distinct peptide sequences +def: "This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001098 +name: confident distinct peptide sequences +def: "This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001099 +name: confident peptide qualification +def: "The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001100 +name: confident peptide sequence number +def: "This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001101 +name: protein group or subset relationship +def: "Protein group or subset relationships." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute + +[Term] +id: MS:1001102 +name: SEQUEST:Chromatogram +is_a: MS:1001006 ! SEQUEST:ViewCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001103 +name: SEQUEST:InfoAndLog +is_a: MS:1001006 ! SEQUEST:ViewCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001104 +name: database UniProtKB/Swiss-Prot +def: "The name of the UniProtKB/Swiss-Prot knowledgebase." [PSI:PI] +is_a: MS:1002126 ! database UniProtKB + +[Term] +id: MS:1001105 +name: peptide sequence-level identification attribute +def: "Peptide level information." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1001106 +name: SEQUEST:TopNumber +def: "Specify \"number\" as value of the CVParam." [PSI:PI] +is_a: MS:1001087 ! SEQUEST:ProcessCV +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001107 +name: data stored in database +def: "Source file for this mzIdentML was a data set in a database." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001108 +name: param: a ion +def: "Parameter information, type of product: a ion with charge on the N-terminal side." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001109 +name: SEQUEST:CullTo +def: "Specify cull string as value of the CVParam." [PSI:PI] +is_a: MS:1001087 ! SEQUEST:ProcessCV +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001110 +name: SEQUEST:modeCV +def: "SEQUEST Mode Input Parameters." [PSI:PI] +is_a: MS:1002096 ! SEQUEST input parameter + +[Term] +id: MS:1001111 +name: SEQUEST:Full +is_a: MS:1001110 ! SEQUEST:modeCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001112 +name: n-terminal flanking residue +def: "Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI] +is_a: MS:1003046 ! peptide-to-protein mapping attribute +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001113 +name: c-terminal flanking residue +def: "Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI] +is_a: MS:1003046 ! peptide-to-protein mapping attribute +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001114 +name: retention time(s) +def: "OBSOLETE Retention time of the spectrum from the source file." [PSI:PI] +comment: This term was made obsolete because scan start time (MS:1000016) should be used instead. +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001115 +name: scan number(s) +def: "OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData." [PSI:PI] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1001116 +name: single protein identification statistic +def: "Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group)." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute + +[Term] +id: MS:1001117 +name: theoretical mass +def: "The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001118 +name: param: b ion +def: "Parameter information, type of product: b ion with charge on the N-terminal side." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001119 +name: param: c ion +def: "Parameter information, type of product: c ion with charge on the N-terminal side." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001120 +name: SEQUEST:FormatAndLinks +is_a: MS:1001110 ! SEQUEST:modeCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001121 +name: number of matched peaks +def: "The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001122 +name: ions series considered +def: "The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb)." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute + +[Term] +id: MS:1001123 +name: number of peaks used +def: "The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001124 +name: number of peaks submitted +def: "The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001125 +name: manual validation +def: "Result of quality estimation: decision of a manual validation." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic +is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001126 +name: SEQUEST:Fast +is_a: MS:1001110 ! SEQUEST:modeCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001127 +name: peptide sharing details +def: "Accessions Containing Sequence - Accessions for each protein containing this peptide." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute + +[Term] +id: MS:1001128 +name: SEQUEST:selectCV +def: "SEQUEST Select Input Parameters." [PSI:PI] +is_a: MS:1002096 ! SEQUEST input parameter + +[Term] +id: MS:1001129 +name: quantification information +def: "Quantification information." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1001130 +name: peptide raw area +def: "OBSOLETE Peptide raw area." [PSI:PI] +comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844). +is_a: MS:1002737 ! peptide-level quantification datatype +is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001131 +name: error on peptide area +def: "Error on peptide area." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001132 +name: peptide ratio +def: "Peptide ratio." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001133 +name: error on peptide ratio +def: "Error on peptide ratio." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001134 +name: protein ratio +def: "Protein ratio." [PSI:PI] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001135 +name: error on protein ratio +def: "Error on protein ratio." [PSI:PI] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001136 +name: p-value (protein diff from 1 randomly) +def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI] +comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855). +is_a: MS:1002738 ! protein-level quantification datatype +is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001137 +name: absolute quantity +def: "Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001138 +name: error on absolute quantity +def: "Error on absolute quantity." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001139 +name: quantitation software name +def: "Quantitation software name." [PSI:PI] +is_a: MS:1000531 ! software +is_a: MS:1001129 ! quantification information + +[Term] +id: MS:1001140 +name: quantitation software version +def: "OBSOLETE Quantitation software version." [PSI:PI] +comment: This term was made obsolete because part of mzQuantML schema. +is_a: MS:1001129 ! quantification information +is_obsolete: true + +[Term] +id: MS:1001141 +name: intensity of precursor ion +def: "The intensity of the precursor ion." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001142 +name: database IPI_human +def: "International Protein Index database for Homo sapiens sequences." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1001143 +name: PSM-level search engine specific statistic +def: "Search engine specific peptide spectrum match scores." [PSI:PI] +is_a: MS:1002347 ! PSM-level identification statistic + +[Term] +id: MS:1001144 +name: SEQUEST:SelectDefault +is_a: MS:1001128 ! SEQUEST:selectCV + +[Term] +id: MS:1001145 +name: SEQUEST:SelectAdvancedCV +def: "SEQUEST Select Advanced Input Parameters." [PSI:PI] +is_a: MS:1001128 ! SEQUEST:selectCV + +[Term] +id: MS:1001146 +name: param: a ion-NH3 DEPRECATED +def: "Ion a-NH3 parameter information, type of product: a ion with lost ammonia." [PSI:PI] +is_a: MS:1001066 ! ions series considered in search + +[Term] +id: MS:1001147 +name: protein ambiguity group result details +is_a: MS:1001085 ! protein-level identification attribute +is_a: MS:1001153 ! search engine specific score + +[Term] +id: MS:1001148 +name: param: a ion-H2O DEPRECATED +def: "Ion a-H2O if a significant and fragment includes STED." [PSI:PI] +is_a: MS:1001066 ! ions series considered in search + +[Term] +id: MS:1001149 +name: param: b ion-NH3 DEPRECATED +def: "Ion b-NH3 parameter information, type of product: b ion with lost ammonia." [PSI:PI] +is_a: MS:1001066 ! ions series considered in search + +[Term] +id: MS:1001150 +name: param: b ion-H2O DEPRECATED +def: "Ion b-H2O if b significant and fragment includes STED." [PSI:PI] +is_a: MS:1001066 ! ions series considered in search + +[Term] +id: MS:1001151 +name: param: y ion-NH3 DEPRECATED +def: "Ion y-NH3 parameter information, type of product: y ion with lost ammonia." [PSI:PI] +is_a: MS:1001066 ! ions series considered in search + +[Term] +id: MS:1001152 +name: param: y ion-H2O DEPRECATED +comment: This term was made obsolete - use MS:1001262 and MS:1002455 instead. +is_a: MS:1001066 ! ions series considered in search + +[Term] +id: MS:1001153 +name: search engine specific score +def: "Search engine specific scores." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1001154 +name: SEQUEST:probability +def: "The SEQUEST result 'Probability'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001155 +name: SEQUEST:xcorr +def: "The SEQUEST result 'XCorr'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001156 +name: SEQUEST:deltacn +def: "The SEQUEST result 'DeltaCn'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001157 +name: SEQUEST:sp +def: "The SEQUEST result 'Sp' (protein)." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001158 +name: SEQUEST:Uniq +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001159 +name: SEQUEST:expectation value +def: "The SEQUEST result 'Expectation value'." [PSI:PI] +is_a: MS:1001153 ! search engine specific score +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001160 +name: SEQUEST:sf +def: "The SEQUEST result 'Sf'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001161 +name: SEQUEST:matched ions +def: "The SEQUEST result 'Matched Ions'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1001162 +name: SEQUEST:total ions +def: "The SEQUEST result 'Total Ions'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1001163 +name: SEQUEST:consensus score +def: "The SEQUEST result 'Consensus Score'." [PSI:PI] +is_a: MS:1001153 ! search engine specific score +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001164 +name: Paragon:unused protscore +def: "The Paragon result 'Unused ProtScore'." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001165 +name: Paragon:total protscore +def: "The Paragon result 'Total ProtScore'." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001166 +name: Paragon:score +def: "The Paragon result 'Score'." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001167 +name: Paragon:confidence +def: "The Paragon result 'Confidence'." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001168 +name: Paragon:expression error factor +def: "The Paragon result 'Expression Error Factor'." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001169 +name: Paragon:expression change p-value +def: "The Paragon result 'Expression change P-value'." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001170 +name: Paragon:contrib +def: "The Paragon result 'Contrib'." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001171 +name: Mascot:score +def: "The Mascot result 'Score'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001172 +name: Mascot:expectation value +def: "The Mascot result 'expectation value'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001173 +name: Mascot:matched ions +def: "The Mascot result 'Matched ions'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001174 +name: Mascot:total ions +def: "The Mascot result 'Total ions'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001175 +name: peptide shared in multiple proteins +def: "A peptide matching multiple proteins." [PSI:PI] +is_a: MS:1001127 ! peptide sharing details + +[Term] +id: MS:1001176 +name: (?<=[KR])(?\!P) +def: "Regular expression for Trypsin." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001177 +name: number of molecular hypothesis considered +def: "Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI] +is_a: MS:1001184 ! search statistics +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001178 +name: database EST +def: "Expressed sequence tag nucleotide sequence database." [PSI:PI] +is_a: MS:1001079 ! database type nucleotide + +[Term] +id: MS:1001180 +name: Cleavage agent regular expression +def: "Regular expressions for cleavage enzymes." [PSI:PI] +relationship: part_of MS:1001044 ! cleavage agent details +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1001184 +name: search statistics +def: "The details of the actual run of the search." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details + +[Term] +id: MS:1001189 +name: modification specificity peptide N-term +def: "As parameter for search engine: apply the modification only at the N-terminus of a peptide." [PSI:PI] +is_a: MS:1001056 ! modification specificity rule + +[Term] +id: MS:1001190 +name: modification specificity peptide C-term +def: "As parameter for search engine: apply the modification only at the C-terminus of a peptide." [PSI:PI] +is_a: MS:1001056 ! modification specificity rule + +[Term] +id: MS:1001191 +name: p-value +def: "OBSOLETE Quality estimation by p-value." [PSI:PI] +comment: This term was made obsolete because now is split into peptide and protein terms. +is_a: MS:1001092 ! peptide sequence-level identification statistic +is_a: MS:1001198 ! protein identification confidence metric +is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001192 +name: Expect value +def: "Result of quality estimation: Expect value." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic +is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001193 +name: confidence score +def: "Result of quality estimation: confidence score." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic +is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001194 +name: quality estimation with decoy database +def: "Quality estimation by decoy database." [PSI:PI] +is_a: MS:1001060 ! quality estimation method details +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001195 +name: decoy DB type reverse +def: "Decoy type: Amino acids of protein sequences are used in reverse order." [PSI:PI] +is_a: MS:1001450 ! decoy DB details + +[Term] +id: MS:1001196 +name: decoy DB type randomized +def: "Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass)." [PSI:PI] +is_a: MS:1001450 ! decoy DB details + +[Term] +id: MS:1001197 +name: DB composition target+decoy +def: "Decoy database composition: database contains original (target) and decoy entries." [PSI:PI] +is_a: MS:1001450 ! decoy DB details + +[Term] +id: MS:1001198 +name: protein identification confidence metric +def: "Identification confidence metric for a protein." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic + +[Term] +id: MS:1001199 +name: Mascot DAT format +def: "Source file for this mzIdentML was in Mascot DAT file format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001200 +name: SEQUEST out file format +def: "Source file for this mzIdentML was in SEQUEST out file format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001201 +name: DB MW filter maximum +def: "Maximum value of molecular weight filter." [PSI:PI] +is_a: MS:1001512 ! Sequence database filters +relationship: has_units UO:0000221 ! dalton +relationship: has_units UO:0000222 ! kilodalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001202 +name: DB MW filter minimum +def: "Minimum value of molecular weight filter." [PSI:PI] +is_a: MS:1001512 ! Sequence database filters +relationship: has_units UO:0000221 ! dalton +relationship: has_units UO:0000222 ! kilodalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001203 +name: DB PI filter maximum +def: "Maximum value of isoelectric point filter." [PSI:PI] +is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001204 +name: DB PI filter minimum +def: "Minimum value of isoelectric point filter." [PSI:PI] +is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001207 +name: Mascot +def: "The name of the Mascot search engine." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001208 +name: SEQUEST +def: "The name of the SEQUEST search engine." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001209 +name: Phenyx +def: "The name of the Phenyx search engine." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001210 +name: mass type settings +def: "The type of mass difference value to be considered by the search engine (monoisotopic or average)." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001211 +name: parent mass type mono +def: "Mass type setting for parent mass was monoisotopic." [PSI:PI] +is_a: MS:1001210 ! mass type settings + +[Term] +id: MS:1001212 +name: parent mass type average +def: "Mass type setting for parent mass was average isotopic." [PSI:PI] +is_a: MS:1001210 ! mass type settings + +[Term] +id: MS:1001213 +name: search result details +def: "OBSOLETE: Scores and global result characteristics." [PSI:PI] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1001214 +name: protein-level global FDR +def: "Estimation of the global false discovery rate of proteins." [PSI:PI] +is_a: MS:1002705 ! protein-level result list statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001215 +name: SEQUEST:PeptideSp +def: "The SEQUEST result 'Sp' in out file (peptide)." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001217 +name: SEQUEST:PeptideRankSp +def: "The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1001218 +name: SEQUEST:PeptideNumber +def: "The SEQUEST result '#' in out file (peptide)." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1001219 +name: SEQUEST:PeptideIdnumber +def: "The SEQUEST result 'Id#' in out file (peptide)." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1001220 +name: frag: y ion +def: "Fragmentation information, type of product: y ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001221 +name: product ion attribute +def: "Fragmentation information like ion types." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1001222 +name: frag: b ion - H2O +def: "Fragmentation information, type of product: b ion without water." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001223 +name: frag: y ion - H2O +def: "Fragmentation information, type of product: y ion without water." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001224 +name: frag: b ion +def: "Fragmentation information, type of product: b ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001225 +name: product ion m/z +def: "The m/z of the product ion." [PSI:PI] +synonym: "fragment ion m/z" EXACT [] +is_a: MS:1001221 ! product ion attribute +relationship: has_units MS:1000040 ! m/z + +[Term] +id: MS:1001226 +name: product ion intensity +def: "The intensity of a single product ion." [PSI:PI] +synonym: "fragment ion intensity" EXACT [] +is_a: MS:1001221 ! product ion attribute +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 + +[Term] +id: MS:1001227 +name: product ion m/z error +def: "The product ion m/z error." [PSI:PI] +is_a: MS:1001221 ! product ion attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_units UO:0000166 ! parts per notation unit +relationship: has_units UO:0000169 ! parts per million + +[Term] +id: MS:1001228 +name: frag: x ion +def: "Fragmentation information, type of product: x ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001229 +name: frag: a ion +def: "Fragmentation information, type of product: a ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001230 +name: frag: z ion +def: "Fragmentation information, type of product: z ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001231 +name: frag: c ion +def: "Fragmentation information, type of product: c ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001232 +name: frag: b ion - NH3 +def: "Ion b-NH3 fragmentation information, type of product: b ion without ammonia." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001233 +name: frag: y ion - NH3 +def: "Ion y-NH3 fragmentation information, type of product: y ion without ammonia." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001234 +name: frag: a ion - H2O +def: "Fragmentation information, type of product: a ion without water." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001235 +name: frag: a ion - NH3 +def: "Ion a-NH3 fragmentation information, type of product: a ion without ammonia." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001236 +name: frag: d ion +def: "Fragmentation information, type of product: d ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001237 +name: frag: v ion +def: "Fragmentation information, type of product: v ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001238 +name: frag: w ion +def: "Fragmentation information, type of product: w ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001239 +name: frag: immonium ion +def: "Fragmentation information, type of product: immonium ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001240 +name: non-identified ion +def: "Non-identified ion." [PSI:PI] +is_a: MS:1001221 ! product ion attribute + +[Term] +id: MS:1001241 +name: co-eluting ion +def: "Co-eluting ion." [PSI:PI] +is_a: MS:1001221 ! product ion attribute + +[Term] +id: MS:1001242 +name: SEQUEST out folder +def: "Source file for this mzIdentML was a SEQUEST folder with its out files." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001243 +name: SEQUEST summary +def: "Source file for this mzIdentML was a SEQUEST summary page (proteins)." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001245 +name: PerSeptive PKS format +def: "PerSeptive peak list file format." [http://www.matrixscience.com/help/data_file_help.html#PKS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001246 +name: SCIEX API III format +def: "PE SCIEX peak list file format." [http://www.matrixscience.com/help/data_file_help.html#API] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001247 +name: Bruker XML format +def: "Bruker data exchange XML format." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001249 +name: search input details +def: "Details describing the search input." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1001250 +name: local FDR +def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic +is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001251 +name: Trypsin +def: "Enzyme trypsin." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P) + +[Term] +id: MS:1001252 +name: DB source EBI +def: "Database source EBI." [PSI:PI] +is_a: MS:1001012 ! database source + +[Term] +id: MS:1001253 +name: DB source NCBI +def: "Database source NCBI." [PSI:PI] +is_a: MS:1001012 ! database source + +[Term] +id: MS:1001254 +name: DB source UniProt +def: "Database source UniProt." [PSI:PI] +is_a: MS:1001012 ! database source + +[Term] +id: MS:1001255 +name: fragment mass type average +def: "Mass type setting for fragment mass was average isotopic." [PSI:PI] +is_a: MS:1001210 ! mass type settings + +[Term] +id: MS:1001256 +name: fragment mass type mono +def: "Mass type setting for fragment mass was monoisotopic." [PSI:PI] +is_a: MS:1001210 ! mass type settings + +[Term] +id: MS:1001257 +name: param: v ion +def: "Parameter information, type of product: side chain loss v ion." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001258 +name: param: d ion +def: "Parameter information, type of product: side chain loss d ion." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001259 +name: param: immonium ion +def: "Parameter information, type of product: immonium ion." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001260 +name: param: w ion +def: "Parameter information, type of product: side chain loss w ion." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001261 +name: param: x ion +def: "Parameter information, type of product: x ion with charge on the C-terminal side." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001262 +name: param: y ion +def: "Parameter information, type of product: y ion with charge on the C-terminal side." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001263 +name: param: z ion +def: "Parameter information, type of product: z ion with charge on the C-terminal side." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001266 +name: role type +def: "Role of a Person or Organization." [PSI:PI] +is_a: MS:1000585 ! contact attribute + +[Term] +id: MS:1001267 +name: software vendor +def: "Software vendor role." [PSI:PI] +is_a: MS:1001266 ! role type + +[Term] +id: MS:1001268 +name: programmer +def: "Programmer role." [PSI:PI] +is_a: MS:1001266 ! role type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001269 +name: instrument vendor +def: "Instrument vendor role." [PSI:PI] +is_a: MS:1001266 ! role type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001270 +name: lab personnel +def: "Lab personnel role." [PSI:PI] +is_a: MS:1001266 ! role type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001271 +name: researcher +def: "Researcher role." [PSI:PI] +is_a: MS:1001266 ! role type + +[Term] +id: MS:1001272 +name: (?<=R)(?\!P) +def: "Regular expression for Arg-C." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001273 +name: (?=[BD]) +def: "Regular expression for Asp-N." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001274 +name: (?=[DE]) +def: "Regular expression for Asp-N-ambic." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001275 +name: ProteinScape SearchEvent +def: "Source data for this mzIdentML was a ProteinScape SearchEvent." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001276 +name: ProteinScape Gel +def: "Source data for this mzIdentML was a ProteinScape Gel." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001283 +name: decoy DB accession regexp +def: "Specify the regular expression for decoy accession numbers." [PSI:PI] +is_a: MS:1001450 ! decoy DB details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001284 +name: decoy DB derived from +def: "OBSOLETE The name of the database, the search database was derived from." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_a: MS:1001450 ! decoy DB details +is_obsolete: true + +[Term] +id: MS:1001285 +name: database IPI_mouse +def: "International Protein Index database for Mus musculus sequences." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1001286 +name: database IPI_rat +def: "International Protein Index database for Rattus norvegicus sequences." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1001287 +name: database IPI_zebrafish +def: "International Protein Index database for Danio rerio sequences." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1001288 +name: database IPI_chicken +def: "International Protein Index database for Gallus gallus sequences." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1001289 +name: database IPI_cow +def: "International Protein Index database for Bos taurus sequences." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1001290 +name: database IPI_arabidopsis +def: "International Protein Index database for Arabidopsis thaliana sequences." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1001291 +name: decoy DB from nr +def: "OBSOLETE Decoy database from a non-redundant GenBank sequence database." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001292 +name: decoy DB from IPI_rat +def: "OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001293 +name: decoy DB from IPI_mouse +def: "OBSOLETE Decoy database from a International Protein Index database for Mus musculus." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001294 +name: decoy DB from IPI_arabidopsis +def: "OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001295 +name: decoy DB from EST +def: "OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001296 +name: decoy DB from IPI_zebrafish +def: "OBSOLETE Decoy database from a International Protein Index database for Danio rerio." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001297 +name: decoy DB from UniProtKB/Swiss-Prot +def: "OBSOLETE Decoy database from a Swiss-Prot protein sequence database." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001298 +name: decoy DB from IPI_chicken +def: "OBSOLETE Decoy database from a International Protein Index database for Gallus gallus." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001299 +name: decoy DB from IPI_cow +def: "OBSOLETE Decoy database from a International Protein Index database for Bos taurus." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001300 +name: decoy DB from IPI_human +def: "OBSOLETE Decoy database from a International Protein Index database for Homo sapiens." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1001301 +name: protein rank +def: "The rank of the protein in a list sorted by the search engine." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001302 +name: search engine specific input parameter +def: "Search engine specific input parameters." [PSI:PI] +is_a: MS:1002093 ! search engine input parameter + +[Term] +id: MS:1001303 +name: Arg-C +def: "Endoproteinase Arg-C." [PSI:PI] +synonym: "Trypsin/R" EXACT [] +synonym: "Clostripain" EXACT [] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001272 ! (?<=R)(?!P) + +[Term] +id: MS:1001304 +name: Asp-N +def: "Endoproteinase Asp-N." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001273 ! (?=[BD]) + +[Term] +id: MS:1001305 +name: Asp-N_ambic +def: "Enzyme Asp-N, Ammonium Bicarbonate (AmBic)." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001274 ! (?=[DE]) + +[Term] +id: MS:1001306 +name: Chymotrypsin +def: "Enzyme chymotrypsin." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P) + +[Term] +id: MS:1001307 +name: CNBr +def: "Cyanogen bromide." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001333 ! (?<=M) + +[Term] +id: MS:1001308 +name: Formic_acid +def: "Formic acid." [PubChem_Compound:284] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001334 ! ((?<=D))|((?=D)) + +[Term] +id: MS:1001309 +name: Lys-C +def: "Endoproteinase Lys-C." [PSI:PI] +synonym: "Trypsin/K" EXACT [] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001335 ! (?<=K)(?!P) + +[Term] +id: MS:1001310 +name: Lys-C/P +def: "Proteinase Lys-C/P." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001336 ! (?<=K) + +[Term] +id: MS:1001311 +name: PepsinA +def: "PepsinA proteinase." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001337 ! (?<=[FL]) + +[Term] +id: MS:1001312 +name: TrypChymo +def: "Cleavage agent TrypChymo." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001338 ! (?<=[FYWLKR])(?!P) + +[Term] +id: MS:1001313 +name: Trypsin/P +def: "Cleavage agent Trypsin/P." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001339 ! (?<=[KR]) + +[Term] +id: MS:1001314 +name: V8-DE +def: "Cleavage agent V8-DE." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001340 ! (?<=[BDEZ])(?!P) + +[Term] +id: MS:1001315 +name: V8-E +def: "Cleavage agent V8-E." [PSI:PI] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001341 ! (?<=[EZ])(?!P) + +[Term] +id: MS:1001316 +name: Mascot:SigThreshold +def: "Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05)." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001317 +name: Mascot:MaxProteinHits +def: "The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001318 +name: Mascot:ProteinScoringMethod +def: "Mascot protein scoring method; either 'Standard' or 'MudPIT'." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001319 +name: Mascot:MinMSMSThreshold +def: "Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001320 +name: Mascot:ShowHomologousProteinsWithSamePeptides +def: "If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001321 +name: Mascot:ShowHomologousProteinsWithSubsetOfPeptides +def: "If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001322 +name: Mascot:RequireBoldRed +def: "Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001323 +name: Mascot:UseUnigeneClustering +def: "If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001324 +name: Mascot:IncludeErrorTolerantMatches +def: "If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included." [http://www.matrixscience.com/help/error_tolerant_help.html] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001325 +name: Mascot:ShowDecoyMatches +def: "If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001326 +name: add_others +def: "OBSOLETE." [PSI:PI] +comment: This former purgatory term was made obsolete. +is_obsolete: true + +[Term] +id: MS:1001328 +name: OMSSA:evalue +def: "OMSSA E-value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001329 +name: OMSSA:pvalue +def: "OMSSA p-value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001330 +name: X\!Tandem:expect +def: "The X!Tandem expectation value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001331 +name: X\!Tandem:hyperscore +def: "The X!Tandem hyperscore." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001332 +name: (?<=[FYWL])(?\!P) +def: "Regular expression for Chymotrypsin." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001333 +name: (?<=M) +def: "Regular expression for CNBr." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001334 +name: ((?<=D))|((?=D)) +def: "Regular expression for formic acid." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001335 +name: (?<=K)(?\!P) +def: "Regular expression for Lys-C." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001336 +name: (?<=K) +def: "Regular expression for Lys-C/P." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001337 +name: (?<=[FL]) +def: "Regular expression for PepsinA." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001338 +name: (?<=[FYWLKR])(?\!P) +def: "Regular expression for TrypChymo." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001339 +name: (?<=[KR]) +def: "Regular expression for Trypsin/P." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001340 +name: (?<=[BDEZ])(?\!P) +def: "Regular expression for V8-DE." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001341 +name: (?<=[EZ])(?\!P) +def: "Regular expression for V8-E." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001342 +name: database sequence details +def: "Details about a single database sequence." [PSI:PI] +is_a: MS:1001011 ! search database details + +[Term] +id: MS:1001343 +name: NA sequence +def: "The sequence is a nucleic acid sequence." [PSI:PI] +is_a: MS:1001342 ! database sequence details + +[Term] +id: MS:1001344 +name: AA sequence +def: "The sequence is a amino acid sequence." [PSI:PI] +is_a: MS:1001342 ! database sequence details + +[Term] +id: MS:1001345 +name: mass table source +def: "Children of this term specify the source of the mass table used." [PSI:PI] +is_a: MS:1001354 ! mass table options + +[Term] +id: MS:1001346 +name: AAIndex mass table +def: "The masses used in the mass table are taken from AAIndex." [PSI:PI] +is_a: MS:1001345 ! mass table source + +[Term] +id: MS:1001347 +name: database file formats +def: "The children of this term define file formats of the sequence database used." [PSI:PI] +is_a: MS:1001011 ! search database details + +[Term] +id: MS:1001348 +name: FASTA format +def: "The sequence database was stored in the FASTA format." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1001349 +name: ASN.1 +def: "The sequence database was stored in the Abstract Syntax Notation 1 format." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1001350 +name: NCBI *.p* +def: "The sequence database was stored in the NCBI formatdb (*.p*) format." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1001351 +name: clustal aln +def: "ClustalW ALN (multiple alignment) format." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1001352 +name: embl em +def: "EMBL entry format." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1001353 +name: NBRF PIR +def: "The NBRF PIR was used as format." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1001354 +name: mass table options +def: "Root node for options for the mass table used." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1001355 +name: peptide descriptions +def: "Descriptions of peptides." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute + +[Term] +id: MS:1001356 +name: spectrum descriptions +def: "Descriptions of the input spectra." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001357 +name: spectrum quality descriptions +def: "Description of the quality of the input spectrum." [PSI:PI] +is_a: MS:1001356 ! spectrum descriptions + +[Term] +id: MS:1001358 +name: msmsEval quality +def: "This term reports the quality of the spectrum assigned by msmsEval." [PSI:PI] +is_a: MS:1001357 ! spectrum quality descriptions +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001359 +name: ambiguous residues +def: "Children of this term describe ambiguous residues." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1001360 +name: alternate single letter codes +def: "List of standard residue one letter codes which are used to replace a non-standard." [PSI:PI] +is_a: MS:1001359 ! ambiguous residues +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001361 +name: alternate mass +def: "List of masses a non-standard letter code is replaced with." [PSI:PI] +is_a: MS:1001359 ! ambiguous residues +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001362 +name: number of unmatched peaks +def: "The number of unmatched peaks." [PSI:PI] +is_a: MS:1002345 ! PSM-level attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001363 +name: peptide unique to one protein +def: "A peptide matching only one." [PSI:PI] +is_a: MS:1001127 ! peptide sharing details + +[Term] +id: MS:1001364 +name: peptide sequence-level global FDR +def: "Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] +is_a: MS:1002703 ! peptide sequence-level result list statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001365 +name: frag: internal yb ion +def: "Fragmentation information, type of product: internal yb ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001366 +name: frag: internal ya ion +def: "Fragmentation information, type of product: internal ya ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001367 +name: frag: z+1 ion +def: "Fragmentation information, type of product: z+1 ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001368 +name: frag: z+2 ion +def: "Fragmentation information, type of product: z+2 ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001369 +name: text format +def: "Simple text file format of \"m/z [intensity]\" values for a PMF (or single MS2) search." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001370 +name: Mascot:homology threshold +def: "The Mascot result 'homology threshold'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001371 +name: Mascot:identity threshold +def: "The Mascot result 'identity threshold'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001372 +name: SEQUEST:Sequences +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001373 +name: SEQUEST:TIC +def: "SEQUEST total ion current." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001374 +name: SEQUEST:Sum +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001375 +name: Phenyx:Instrument Type +def: "The instrument type parameter value in Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001376 +name: Phenyx:Scoring Model +def: "The selected scoring model in Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001377 +name: Phenyx:Default Parent Charge +def: "The default parent charge value in Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001378 +name: Phenyx:Trust Parent Charge +def: "The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001379 +name: Phenyx:Turbo +def: "The turbo mode parameter in Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001380 +name: Phenyx:Turbo:ErrorTol +def: "The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001381 +name: Phenyx:Turbo:Coverage +def: "The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001382 +name: Phenyx:Turbo:Series +def: "The list of ion series considered in the turbo mode of Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001383 +name: Phenyx:MinPepLength +def: "The minimal number of residues for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001384 +name: Phenyx:MinPepzscore +def: "The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001385 +name: Phenyx:MaxPepPvalue +def: "The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001386 +name: Phenyx:AC Score +def: "The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001387 +name: Phenyx:Conflict Resolution +def: "The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used." [PSI:PI] +is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001388 +name: Phenyx:AC +def: "The primary sequence database identifier of a protein in Phenyx." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001389 +name: Phenyx:ID +def: "A secondary sequence database identifier of a protein in Phenyx." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001390 +name: Phenyx:Score +def: "The protein score of a protein match in Phenyx." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001391 +name: Phenyx:Peptides1 +def: "First number of phenyx result \"#Peptides\"." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001392 +name: Phenyx:Peptides2 +def: "Second number of phenyx result \"#Peptides\"." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001393 +name: Phenyx:Auto +def: "The value of the automatic peptide acceptance filter in Phenyx." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001394 +name: Phenyx:User +def: "The value of the user-defined peptide acceptance filter in Phenyx." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001395 +name: Phenyx:Pepzscore +def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001396 +name: Phenyx:PepPvalue +def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001397 +name: Phenyx:NumberOfMC +def: "The number of missed cleavages of a peptide sequence in Phenyx." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001398 +name: Phenyx:Modif +def: "The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001399 +name: OMSSA csv format +def: "Source file for this mzIdentML was in OMSSA csv file format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001400 +name: OMSSA xml format +def: "Source file for this mzIdentML was in OMSSA xml file format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001401 +name: X\!Tandem xml format +def: "Source file for this mzIdentML was in X!Tandem xml file format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001405 +name: spectrum identification result details +def: "This subsection describes terms which can describe details of spectrum identification results." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1001406 +name: param: internal yb ion +def: "Parameter information, type of product: internal yb ion." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001407 +name: param: internal ya ion +def: "Parameter information, type of product: internal ya ion." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001408 +name: param: z+1 ion +def: "Parameter information, type of product: z+1 ion." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001409 +name: param: z+2 ion +def: "Parameter information, type of product: z+2 ion." [PSI:PI] +is_a: MS:1002473 ! ion series considered in search + +[Term] +id: MS:1001410 +name: translation start codons +def: "The translation start codons used to translate the nucleotides to amino acids." [PSI:PI] +is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001411 +name: search tolerance specification +def: "Specification of the search tolerance." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001412 +name: search tolerance plus value +is_a: MS:1001411 ! search tolerance specification +relationship: has_units UO:0000166 ! parts per notation unit +relationship: has_units UO:0000169 ! parts per million +relationship: has_units UO:0000187 ! percent +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001413 +name: search tolerance minus value +is_a: MS:1001411 ! search tolerance specification +relationship: has_units UO:0000166 ! parts per notation unit +relationship: has_units UO:0000169 ! parts per million +relationship: has_units UO:0000187 ! percent +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001414 +name: MGF scans +def: "OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details +is_obsolete: true +replaced_by: MS:1000797 +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001415 +name: MGF raw scans +def: "OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details +is_obsolete: true +replaced_by: MS:1000798 +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001416 +name: spectrum title +def: "OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details +is_obsolete: true +replaced_by: MS:1000796 +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001417 +name: SpectraST:dot +def: "SpectraST dot product of two spectra, measuring spectral similarity." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001418 +name: SpectraST:dot_bias +def: "SpectraST measure of how much of the dot product is dominated by a few peaks." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001419 +name: SpectraST:discriminant score F +def: "SpectraST spectrum score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001420 +name: SpectraST:delta +def: "SpectraST normalised difference between dot product of top hit and runner-up." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001421 +name: pepXML format +def: "The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001422 +name: protXML format +def: "The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001423 +name: translation table description +def: "A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI] +is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1001424 +name: ProteinExtractor:Methodname +def: "Name of the used method in the ProteinExtractor algorithm." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001425 +name: ProteinExtractor:GenerateNonRedundant +def: "Flag indicating if a non redundant scoring should be generated." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001426 +name: ProteinExtractor:IncludeIdentified +def: "Flag indicating if identified proteins should be included." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001427 +name: ProteinExtractor:MaxNumberOfProteins +def: "The maximum number of proteins to consider." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001428 +name: ProteinExtractor:MaxProteinMass +def: "The maximum considered mass for a protein." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001429 +name: ProteinExtractor:MinNumberOfPeptides +def: "The minimum number of proteins to consider." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001430 +name: ProteinExtractor:UseMascot +def: "Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001431 +name: ProteinExtractor:MascotPeptideScoreThreshold +def: "Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001432 +name: ProteinExtractor:MascotUniqueScore +def: "In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001433 +name: ProteinExtractor:MascotUseIdentityScore +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001434 +name: ProteinExtractor:MascotWeighting +def: "Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001435 +name: ProteinExtractor:UseSequest +def: "Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001436 +name: ProteinExtractor:SequestPeptideScoreThreshold +def: "Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001437 +name: ProteinExtractor:SequestUniqueScore +def: "In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001438 +name: ProteinExtractor:SequestWeighting +def: "Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001439 +name: ProteinExtractor:UseProteinSolver +def: "Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001440 +name: ProteinExtractor:ProteinSolverPeptideScoreThreshold +def: "Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001441 +name: ProteinExtractor:ProteinSolverUniqueScore +def: "In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001442 +name: ProteinExtractor:ProteinSolverWeighting +def: "Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001443 +name: ProteinExtractor:UsePhenyx +def: "Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score." [PSI:PI] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001444 +name: ProteinExtractor:PhenyxPeptideScoreThreshold +def: "Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001445 +name: ProteinExtractor:PhenyxUniqueScore +def: "In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001446 +name: ProteinExtractor:PhenyxWeighting +def: "Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001447 +name: prot:FDR threshold +def: "False-discovery rate threshold for proteins." [PSI:PI] +is_a: MS:1002485 ! protein-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001448 +name: pep:FDR threshold +def: "False-discovery rate threshold for peptides." [PSI:PI] +is_a: MS:1002484 ! peptide-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001449 +name: OMSSA e-value threshold +def: "Threshold for OMSSA e-value for quality estimation." [PSI:PI] +is_a: MS:1002099 ! OMSSA input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001450 +name: decoy DB details +def: "Details of decoy generation and database structure." [PSI:PI] +is_a: MS:1001011 ! search database details + +[Term] +id: MS:1001451 +name: decoy DB generation algorithm +def: "Name of algorithm used for decoy generation." [PSI:PI] +is_a: MS:1001450 ! decoy DB details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001452 +name: decoy DB type shuffle +def: "Decoy type: Amino acids of protein sequences are used in a random order." [PSI:PI] +is_a: MS:1001450 ! decoy DB details + +[Term] +id: MS:1001453 +name: DB composition only decoy +def: "Decoy database composition: database contains only decoy entries." [PSI:PI] +is_a: MS:1001450 ! decoy DB details + +[Term] +id: MS:1001454 +name: quality estimation with implicite decoy sequences +def: "Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy)." [PSI:PI] +is_a: MS:1001060 ! quality estimation method details + +[Term] +id: MS:1001455 +name: acquisition software +def: "Acquisition software." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1001456 +name: analysis software +def: "Analysis software." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1001457 +name: data processing software +def: "Data processing software." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1001458 +name: spectrum generation information +def: "Vocabularies describing the spectrum generation information." [PSI:PI] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1001459 +name: file format +def: "Format of data files." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1001460 +name: unknown modification +def: "This term should be given if the modification was unknown." [PSI:PI] +is_a: MS:1001471 ! peptide modification details + +[Term] +id: MS:1001461 +name: greylag +def: "Greylag identification software." [http://greylag.org/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001462 +name: PEFF format +def: "The sequence database was stored in the PEFF (PSI enhanced FastA file) format." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1001463 +name: Phenyx XML format +def: "Phenyx open XML file format." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001464 +name: DTASelect format +def: "DTASelect file format." [PMID:12643522, http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001466 +name: MS2 format +def: "MS2 file format for MS2 spectral data." [PMID:15317041, DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001467 +name: taxonomy: NCBI TaxID +def: "This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens." [PSI:PI] +is_a: MS:1001089 ! molecule taxonomy +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001468 +name: taxonomy: common name +def: "This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] +is_a: MS:1001089 ! molecule taxonomy +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001469 +name: taxonomy: scientific name +def: "This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] +is_a: MS:1001089 ! molecule taxonomy +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001470 +name: taxonomy: Swiss-Prot ID +def: "This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] +is_a: MS:1001089 ! molecule taxonomy +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001471 +name: peptide modification details +def: "The children of this term can be used to describe modifications." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1001472 +name: selected ion monitoring chromatogram +def: "Representation of an array of the measurements of a selectively monitored ion versus time." [PSI:MS] +synonym: "SIM chromatogram" EXACT [] +is_a: MS:1000810 ! ion current chromatogram + +[Term] +id: MS:1001473 +name: selected reaction monitoring chromatogram +def: "Representation of an array of the measurements of a selectively monitored reaction versus time." [PSI:MS] +synonym: "SRM chromatogram" EXACT [] +is_a: MS:1000810 ! ion current chromatogram + +[Term] +id: MS:1001474 +name: consecutive reaction monitoring chromatogram +def: "OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time." [PSI:MS] +comment: This term was made obsolete because, by design, it can't be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way. +synonym: "CRM chromatogram" EXACT [] +is_a: MS:1000810 ! ion current chromatogram +is_obsolete: true + +[Term] +id: MS:1001475 +name: OMSSA +def: "Open Mass Spectrometry Search Algorithm was used to analyze the spectra." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001476 +name: X\!Tandem +def: "X!Tandem was used to analyze the spectra." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001477 +name: SpectraST +def: "Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline." [PSI:PI] +is_a: MS:1001456 ! analysis software +is_a: MS:1003207 ! library creation software + +[Term] +id: MS:1001478 +name: Mascot Parser +def: "Mascot Parser was used to analyze the spectra." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001479 +name: null-terminated ASCII string +def: "Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte." [PSI:MS] +is_a: MS:1000518 ! binary data type + +[Term] +id: MS:1001480 +name: SCIEX TOF/TOF nativeID format +def: "Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1001481 +name: SCIEX TOF/TOF database +def: "Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001482 +name: 5800 TOF/TOF +def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1001483 +name: SCIEX TOF/TOF Series Explorer Software +def: "SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis." [PSI:MS] +is_a: MS:1000690 ! SCIEX software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001484 +name: intensity normalization +def: "Normalization of data point intensities." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1001485 +name: m/z calibration +def: "Calibration of data point m/z positions." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1001486 +name: data filtering +def: "Filtering out part of the data." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1001487 +name: ProteinExtractor +def: "An algorithm for protein determination/assembly integrated into Bruker's ProteinScape." [PSI:MS] +is_a: MS:1000692 ! Bruker software +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001488 +name: Mascot Distiller +def: "Mascot Distiller." [PSI:PI] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001489 +name: Mascot Integra +def: "Mascot Integra." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001490 +name: Percolator +def: "Percolator." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001491 +name: percolator:Q value +def: "Percolator:Q value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001492 +name: percolator:score +def: "Percolator:score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001493 +name: percolator:PEP +def: "Posterior error probability." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001494 +name: no threshold +def: "In case no threshold was used." [PSI:PI] +is_a: MS:1002482 ! statistical threshold + +[Term] +id: MS:1001495 +name: ProteinScape:SearchResultId +def: "The SearchResultId of this peptide as SearchResult in the ProteinScape database." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001496 +name: ProteinScape:SearchEventId +def: "The SearchEventId of the SearchEvent in the ProteinScape database." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001497 +name: ProteinScape:ProfoundProbability +def: "The Profound probability score stored by ProteinScape." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001498 +name: Profound:z value +def: "The Profound z value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001499 +name: Profound:Cluster +def: "The Profound cluster score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001500 +name: Profound:ClusterRank +def: "The Profound cluster rank." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001501 +name: MSFit:Mowse score +def: "The MSFit Mowse score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001502 +name: Sonar:Score +def: "The Sonar score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001503 +name: ProteinScape:PFFSolverExp +def: "The ProteinSolver exp value stored by ProteinScape." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001504 +name: ProteinScape:PFFSolverScore +def: "The ProteinSolver score stored by ProteinScape." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001505 +name: ProteinScape:IntensityCoverage +def: "The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001506 +name: ProteinScape:SequestMetaScore +def: "The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001507 +name: ProteinExtractor:Score +def: "The score calculated by ProteinExtractor." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001508 +name: Agilent MassHunter nativeID format +def: "Native format defined by scanId=xsd:nonNegativeInteger." [PSI:PI] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1001509 +name: Agilent MassHunter format +def: "A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001510 +name: TSQ Vantage +def: "TSQ Vantage." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1001511 +name: Sequence database filter types +def: "Filter types which are used to filter a sequence database." [PSI:PI] +is_a: MS:1001019 ! database filtering + +[Term] +id: MS:1001512 +name: Sequence database filters +def: "Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search." [PSI:PI] +is_a: MS:1001019 ! database filtering + +[Term] +id: MS:1001513 +name: DB sequence filter pattern +def: "DB sequence filter pattern." [PSI:MS] +is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001514 +name: DB accession filter string +def: "DB accession filter string." [PSI:MS] +is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001515 +name: frag: c ion - H2O +def: "Fragmentation information, type of product: c ion without water." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001516 +name: frag: c ion - NH3 +def: "Fragmentation information, type of product: c ion without ammonia." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001517 +name: frag: z ion - H2O +def: "Fragmentation information, type of product: z ion without water." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001518 +name: frag: z ion - NH3 +def: "Fragmentation information, type of product: z ion without ammonia." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001519 +name: frag: x ion - H2O +def: "Fragmentation information, type of product: x ion without water." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001520 +name: frag: x ion - NH3 +def: "Fragmentation information, type of product: x ion without ammonia." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001521 +name: frag: precursor ion - H2O +def: "Fragmentation information, type of product: precursor ion without water." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001522 +name: frag: precursor ion - NH3 +def: "Fragmentation information, type of product: precursor ion without ammonia." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001523 +name: frag: precursor ion +def: "Fragmentation information, type of product: precursor ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1001524 +name: fragment neutral loss +def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001525 +name: precursor neutral loss +def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001526 +name: spectrum from database integer nativeID format +def: "Native format defined by databasekey=xsd:long." [PSI:MS] +comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1001527 +name: Proteinscape spectra +def: "Spectra from Bruker/Protagen Proteinscape database." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001528 +name: Mascot query number +def: "Native format defined by query=xsd:nonNegativeInteger." [PSI:MS] +comment: The spectrum (query) number in a Mascot results file, starting from 1. +is_a: MS:1000767 ! native spectrum identifier format +is_a: MS:1001405 ! spectrum identification result details + +[Term] +id: MS:1001529 +name: spectra data details +def: "Child-terms contain information to map the results back to spectra." [PSI:MS] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1001530 +name: mzML unique identifier +def: "Native format defined by mzMLid=xsd:IDREF." [PSI:MS] +comment: A unique identifier of a spectrum stored in an mzML file. +is_a: MS:1001529 ! spectra data details + +[Term] +id: MS:1001531 +name: spectrum from ProteinScape database nativeID format +def: "Native format defined by databasekey=xsd:long." [PSI:MS] +comment: A unique identifier of a spectrum stored in a ProteinScape database. +is_a: MS:1000767 ! native spectrum identifier format +is_a: MS:1001529 ! spectra data details + +[Term] +id: MS:1001532 +name: spectrum from database string nativeID format +def: "Native format defined by databasekey=xsd:string." [PSI:MS] +comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). +is_a: MS:1000767 ! native spectrum identifier format +is_a: MS:1001529 ! spectra data details + +[Term] +id: MS:1001533 +name: Bruker Daltonics esquire series +def: "Bruker Daltonics' esquire series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1001534 +name: Bruker Daltonics flex series +def: "Bruker Daltonics' flex series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1001535 +name: Bruker Daltonics BioTOF series +def: "Bruker Daltonics' BioTOF series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1001536 +name: Bruker Daltonics micrOTOF series +def: "Bruker Daltonics' micrOTOF series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1001537 +name: BioTOF +def: "Bruker Daltonics' BioTOF: ESI TOF." [PSI:MS] +is_a: MS:1001535 ! Bruker Daltonics BioTOF series + +[Term] +id: MS:1001538 +name: BioTOF III +def: "Bruker Daltonics' BioTOF III: ESI TOF." [PSI:MS] +is_a: MS:1001535 ! Bruker Daltonics BioTOF series + +[Term] +id: MS:1001539 +name: UltroTOF-Q +def: "Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional)." [PSI:MS] +is_a: MS:1001535 ! Bruker Daltonics BioTOF series + +[Term] +id: MS:1001540 +name: micrOTOF II +def: "Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1001541 +name: maXis +def: "Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] +is_a: MS:1001547 ! Bruker Daltonics maXis series + +[Term] +id: MS:1001542 +name: amaZon ETD +def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR." [PSI:MS] +is_a: MS:1001545 ! Bruker Daltonics amaZon series + +[Term] +id: MS:1001543 +name: microflex LRF +def: "Bruker Daltonics' microflex LRF: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1001544 +name: ultrafleXtreme +def: "Bruker Daltonics' ultrafleXtreme: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1001545 +name: Bruker Daltonics amaZon series +def: "Bruker Daltonics' amaZon series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1001546 +name: amaZon X +def: "Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS] +is_a: MS:1001545 ! Bruker Daltonics amaZon series + +[Term] +id: MS:1001547 +name: Bruker Daltonics maXis series +def: "Bruker Daltonics' maXis series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1001548 +name: Bruker Daltonics solarix series +def: "Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1001549 +name: solariX +def: "Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR." [PSI:MS] +is_a: MS:1001548 ! Bruker Daltonics solarix series + +[Term] +id: MS:1001550 +name: microflex II +def: "Bruker Daltonics' microflex II: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1001553 +name: autoflex II TOF/TOF +def: "Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1001554 +name: autoflex III TOF/TOF smartbeam +def: "Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1001555 +name: autoflex +def: "Bruker Daltonics' autoflex: MALDI TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1001556 +name: Bruker Daltonics apex series +def: "Bruker Daltonics' apex series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1001557 +name: Shimadzu Corporation software +def: "Shimadzu Corporation software." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1001558 +name: MALDI Solutions +def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS] +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software +is_a: MS:1001557 ! Shimadzu Corporation software + +[Term] +id: MS:1001559 +name: SCIEX TOF/TOF T2D nativeID format +def: "Native format defined by file=xsd:IDREF." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1001560 +name: SCIEX TOF/TOF T2D format +def: "Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001561 +name: Scaffold +def: "Scaffold analysis software." [http://www.proteomesoftware.com] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001562 +name: Scaffold nativeID format +def: "Scaffold native ID format." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1001563 +name: SEQUEST SQT format +def: "Source file for this mzIdentML was in SEQUEST SQT format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001564 +name: Discoverer MSF format +def: "Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001565 +name: IdentityE XML format +def: "Source file for this mzIdentML was in Waters IdentityE XML format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001566 +name: ProteinLynx XML format +def: "Source file for this mzIdentML was in Waters ProteinLynx XML format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001567 +name: SpectrumMill directories +def: "Source file for this mzIdentML was in Agilent SpectrumMill directory format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1001568 +name: Scaffold:Peptide Probability +def: "Scaffold peptide probability score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001569 +name: IdentityE Score +def: "Waters IdentityE peptide score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001570 +name: ProteinLynx:Log Likelihood +def: "ProteinLynx log likelihood score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001571 +name: ProteinLynx:Ladder Score +def: "Waters ProteinLynx Ladder score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001572 +name: SpectrumMill:Score +def: "Spectrum mill peptide score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001573 +name: SpectrumMill:SPI +def: "SpectrumMill SPI score (%)." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001574 +name: report only spectra assigned to identified proteins +def: "Flag indicating to report only the spectra assigned to identified proteins." [PSI:PI] +is_a: MS:1001060 ! quality estimation method details + +[Term] +id: MS:1001575 +name: Scaffold: Minimum Peptide Count +def: "Minimum number of peptides a protein must have to be accepted." [PSI:PI] +is_a: MS:1002106 ! Scaffold input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001576 +name: Scaffold: Minimum Protein Probability +def: "Minimum protein probability a protein must have to be accepted." [PSI:PI] +is_a: MS:1002106 ! Scaffold input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001577 +name: Scaffold: Minimum Peptide Probability +def: "Minimum probability a peptide must have to be accepted for protein scoring." [PSI:PI] +is_a: MS:1002106 ! Scaffold input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001578 +name: minimum number of enzymatic termini +def: "Minimum number of enzymatic termini a peptide must have to be accepted." [PSI:PI] +is_a: MS:1002094 ! common search engine input parameter +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001579 +name: Scaffold:Protein Probability +def: "Scaffold protein probability score." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001580 +name: SpectrumMill:Discriminant Score +def: "Discriminant score from Agilent SpectrumMill software." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001581 +name: FAIMS compensation voltage +def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] +synonym: "FAIMS CV" EXACT [] +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001582 +name: XCMS +def: "Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data." [PSI:MS] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001583 +name: MaxQuant +def: "MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001584 +name: combined pmf + ms-ms search +def: "Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF)." [PSI:MS] +is_a: MS:1001080 ! search type + +[Term] +id: MS:1001585 +name: MyriMatch +def: "Tabb Lab software for directly comparing peptides in a database to tandem mass spectra." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001586 +name: DirecTag +def: "Tabb Lab software for generating sequence tags from tandem mass spectra." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001587 +name: TagRecon +def: "Tabb Lab software for reconciling sequence tags to a protein database." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001588 +name: Pepitome +def: "Tabb Lab software for spectral library searches on tandem mass spectra." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001589 +name: MyriMatch:MVH +def: "Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance." [PSI:MS] +synonym: "Pepitome:MVH" EXACT [] +synonym: "TagRecon:MVH" EXACT [] +is_a: MS:1001143 ! PSM-level search engine specific statistic + +[Term] +id: MS:1001590 +name: MyriMatch:mzFidelity +def: "The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution." [PSI:MS] +synonym: "Pepitome:mzFidelity" EXACT [] +synonym: "TagRecon:mzFidelity" EXACT [] +is_a: MS:1001143 ! PSM-level search engine specific statistic + +[Term] +id: MS:1001591 +name: anchor protein +def: "A representative protein selected from a set of sequence same-set or spectrum same-set proteins." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001592 +name: family member protein +def: "A protein with significant homology to another protein, but some distinguishing peptide matches." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001593 +name: group member with undefined relationship OR ortholog protein +def: "TO ENDETAIL: a really generic relationship OR ortholog protein." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship + +[Term] +id: MS:1001594 +name: sequence same-set protein +def: "A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001595 +name: spectrum same-set protein +def: "A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001596 +name: sequence sub-set protein +def: "A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001597 +name: spectrum sub-set protein +def: "A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001598 +name: sequence subsumable protein +def: "A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001599 +name: spectrum subsumable protein +def: "A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001600 +name: protein inference confidence category +def: "Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable)." [PSI:MS] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001601 +name: ProteomeDiscoverer:Spectrum Files:Raw File names +def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS] +comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001602 +name: ProteomeDiscoverer:SRF File Selector:SRF File Path +def: "OBSOLETE Path and name of the .srf (SEQUEST Result Format) file." [PSI:MS] +comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001603 +name: ProteomeDiscoverer:Spectrum Selector:Ionization Source +def: "OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001604 +name: ProteomeDiscoverer:Activation Type +def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001605 +name: ProteomeDiscoverer:Spectrum Selector:Lower RT Limit +def: "Lower retention-time limit." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001606 +name: ProteomeDiscoverer:Mass Analyzer +def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001607 +name: ProteomeDiscoverer:Max Precursor Mass +def: "Maximum mass limit of a singly charged precursor ion." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001608 +name: ProteomeDiscoverer:Min Precursor Mass +def: "Minimum mass limit of a singly charged precursor ion." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001609 +name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count +def: "Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001610 +name: ProteomeDiscoverer:MS Order +def: "OBSOLETE Level of the mass spectrum (MS2 ... MS10)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001611 +name: ProteomeDiscoverer:Polarity Mode +def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001612 +name: ProteomeDiscoverer:Spectrum Selector:Precursor Selection +def: "Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3)." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001613 +name: ProteomeDiscoverer:SN Threshold +def: "Signal-to-Noise ratio below which peaks are removed." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001614 +name: ProteomeDiscoverer:Scan Type +def: "OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS] +comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001615 +name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold +def: "Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001616 +name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements +def: "Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001617 +name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements +def: "Specifies the charge state of the precursor ions, if it is not defined in the scan header." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001618 +name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements +def: "Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001619 +name: ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements +def: "Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001620 +name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements +def: "Specifies the polarity of the ions monitored if it is not included in the scan header." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001621 +name: ProteomeDiscoverer:Spectrum Selector:Upper RT Limit +def: "Upper retention-time limit." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001622 +name: ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset +def: "Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001623 +name: ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass +def: "Maximum allowed mass of a neutral loss." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001624 +name: ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor +def: "Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001625 +name: ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks +def: "Determines whether neutral loss peaks are removed from ETD and ECD spectra." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001626 +name: ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses +def: "Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001627 +name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones +def: "Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001628 +name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak +def: "Determines whether precursor artifact peaks from the MS2 input spectra are removed." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001629 +name: ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch +def: "Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001630 +name: ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch +def: "Determines whether spectra from different MS order scans can be grouped together." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001631 +name: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference +def: "OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species." [PSI:MS] +comment: This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001632 +name: ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion +def: "Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001633 +name: ProteomeDiscoverer:Xtract:Highest Charge +def: "Highest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001634 +name: ProteomeDiscoverer:Xtract:Highest MZ +def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS] +comment: This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001635 +name: ProteomeDiscoverer:Xtract:Lowest Charge +def: "Lowest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001636 +name: ProteomeDiscoverer:Xtract:Lowest MZ +def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS] +comment: This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001637 +name: ProteomeDiscoverer:Xtract:Monoisotopic Mass Only +def: "Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001638 +name: ProteomeDiscoverer:Xtract:Overlapping Remainder +def: "Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted)." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001639 +name: ProteomeDiscoverer:Xtract:Required Fitting Accuracy +def: "Accuracy required for a pattern fit to be considered valid." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001640 +name: ProteomeDiscoverer:Xtract:Resolution At 400 +def: "Resolution at mass 400." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001641 +name: ProteomeDiscoverer:Lowest Charge State +def: "Minimum charge state below which peptides are filtered out." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001642 +name: ProteomeDiscoverer:Highest Charge State +def: "Maximum charge above which peptides are filtered out." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001643 +name: ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores +def: "Determines whether spectra with scores above the threshold score are retained rather than filtered out." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001644 +name: ProteomeDiscoverer:Dynamic Modification +def: "Determine dynamic post-translational modifications (PTMs)." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001645 +name: ProteomeDiscoverer:Static Modification +def: "Static Modification to all occurrences of a named amino acid." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001646 +name: ProteomeDiscoverer:Mascot:Decoy Search +def: "OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database." [PSI:MS] +comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001647 +name: ProteomeDiscoverer:Mascot:Error tolerant Search +def: "Determines whether to search error-tolerant." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001648 +name: ProteomeDiscoverer:Mascot:Max MGF File Size +def: "Maximum size of the .mgf (Mascot Generic Format) file in MByte." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001649 +name: ProteomeDiscoverer:Mascot:Mascot Server URL +def: "URL (Uniform resource Locator) of the Mascot server." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001650 +name: ProteomeDiscoverer:Mascot:Number of attempts to submit the search +def: "Number of attempts to submit the Mascot search." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001651 +name: ProteomeDiscoverer:Mascot:X Static Modification +def: "Number of attempts to submit the Mascot search." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001652 +name: ProteomeDiscoverer:Mascot:User Name +def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS] +comment: This term was made obsolete because it's recommended to use researcher (MS:1001271) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001653 +name: ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search +def: "Time interval between attempts to submit a search in seconds." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001654 +name: ProteomeDiscoverer:Enzyme Name +def: "OBSOLETE Specifies the enzyme reagent used for protein digestion." [PSI:MS] +comment: This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001655 +name: ProteomeDiscoverer:Fragment Mass Tolerance +def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu." [PSI:MS] +comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001656 +name: Mascot:Instrument +def: "Type of instrument used to acquire the data in the raw file." [PSI:MS] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001657 +name: ProteomeDiscoverer:Maximum Missed Cleavage Sites +def: "Maximum number of missed cleavage sites to consider during the digest." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001658 +name: ProteomeDiscoverer:Mascot:Peptide CutOff Score +def: "Minimum score in the IonScore column that each peptide must exceed in order to be reported." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001659 +name: ProteomeDiscoverer:Precursor Mass Tolerance +def: "OBSOLETE Mass window for which precursor ions are considered to be the same species." [PSI:MS] +comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001660 +name: ProteomeDiscoverer:Mascot:Protein CutOff Score +def: "Minimum protein score in the IonScore column that each protein must exceed in order to be reported." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001661 +name: ProteomeDiscoverer:Protein Database +def: "OBSOLETE Database to use in the search (configured on the Mascot server)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use database name (MS:1001013) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001662 +name: ProteomeDiscoverer:Mascot:Protein Relevance Factor +def: "Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001663 +name: ProteomeDiscoverer:Target FDR Relaxed +def: "Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001664 +name: ProteomeDiscoverer:Target FDR Strict +def: "Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001665 +name: ProteomeDiscoverer:Mascot:Taxonomy +def: "OBSOLETE Limits searches to entries from a particular species or group of species." [PSI:MS] +comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001666 +name: ProteomeDiscoverer:Use Average Precursor Mass +def: "OBSOLETE Use average mass for the precursor." [PSI:MS] +comment: This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001667 +name: Mascot:use MudPIT scoring +def: "OBSOLETE Determines whether to use MudPIT or normal scoring." [PSI:MS] +comment: This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead. +is_a: MS:1002095 ! Mascot input parameter +is_obsolete: true +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001668 +name: ProteomeDiscoverer:Absolute XCorr Threshold +def: "Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001669 +name: ProteomeDiscoverer:SEQUEST:Calculate Probability Score +def: "Determines whether to calculate a probability score for every peptide match." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001670 +name: ProteomeDiscoverer:SEQUEST:CTerminal Modification +def: "Dynamic C-terminal modification that is used during the search." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001671 +name: ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage +def: "Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001672 +name: ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide +def: "Maximum number of identical modifications that a single peptide can have." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001673 +name: ProteomeDiscoverer:Max Modifications Per Peptide +def: "Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001674 +name: ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered +def: "Maximum number of peptides that are searched and scored per spectrum." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001675 +name: ProteomeDiscoverer:Maximum Peptides Output +def: "Maximum number of peptide matches reported per spectrum." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001676 +name: ProteomeDiscoverer:Maximum Protein References Per Peptide +def: "Maximum number of proteins that a single identified peptide can be associated with during protein assembly." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001677 +name: ProteomeDiscoverer:SEQUEST:NTerminal Modification +def: "Dynamic N-terminal modification that is used during the search." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001678 +name: ProteomeDiscoverer:Peptide CTerminus +def: "Static modification for the C terminal of the peptide used during the search." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001679 +name: ProteomeDiscoverer:Peptide NTerminus +def: "Static modification for the N terminal of the peptide used during the search." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001680 +name: ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor +def: "Specifies a factor to apply to the protein score." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001681 +name: ProteomeDiscoverer:Protein Relevance Threshold +def: "Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001682 +name: ProteomeDiscoverer:Search Against Decoy Database +def: "OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database." [PSI:MS] +comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001683 +name: ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses +def: "Use average masses for the fragments." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001684 +name: ProteomeDiscoverer:Use Neutral Loss a Ions +def: "Determines whether a ions with neutral loss are used for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001685 +name: ProteomeDiscoverer:Use Neutral Loss b Ions +def: "Determines whether b ions with neutral loss are used for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001686 +name: ProteomeDiscoverer:Use Neutral Loss y Ions +def: "Determines whether y ions with neutral loss are used for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001687 +name: ProteomeDiscoverer:Use Neutral Loss z Ions +def: "Determines whether z ions with neutral loss are used for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001688 +name: ProteomeDiscoverer:SEQUEST:Weight of a Ions +def: "Uses a ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001689 +name: ProteomeDiscoverer:SEQUEST:Weight of b Ions +def: "Uses b ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001690 +name: ProteomeDiscoverer:SEQUEST:Weight of c Ions +def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001691 +name: ProteomeDiscoverer:SEQUEST:Weight of d Ions +def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001692 +name: ProteomeDiscoverer:SEQUEST:Weight of v Ions +def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001693 +name: ProteomeDiscoverer:SEQUEST:Weight of w Ions +def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001694 +name: ProteomeDiscoverer:SEQUEST:Weight of x Ions +def: "Uses x ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001695 +name: ProteomeDiscoverer:SEQUEST:Weight of y Ions +def: "Uses y ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001696 +name: ProteomeDiscoverer:SEQUEST:Weight of z Ions +def: "Uses z ions for spectrum matching with this relative factor." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001697 +name: ProteomeDiscoverer:ZCore:Protein Score Cutoff +def: "Sets a minimum protein score that each protein must exceed in order to be reported." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001698 +name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method +def: "Specifies which peak to select if more than one peak is found inside the integration window." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001699 +name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance +def: "Specifies the mass-to-charge window that enables one to look for the reporter peaks." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001700 +name: ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method +def: "Quantitation method for isobarically labeled quantitation." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001701 +name: ProteomeDiscoverer:Spectrum Exporter:Export Format +def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001702 +name: ProteomeDiscoverer:Spectrum Exporter:File name +def: "Name of the output file that contains the exported data." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001703 +name: ProteomeDiscoverer:Search Modifications Only For Identified Proteins +def: "Influences the modifications search." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001704 +name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1 +def: "Standard high confidence XCorr parameter for charge = 1." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001705 +name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2 +def: "Standard high confidence XCorr parameter for charge = 2." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001706 +name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3 +def: "Standard high confidence XCorr parameter for charge = 3." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001707 +name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4 +def: "Standard high confidence XCorr parameter for charge >= 4." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001708 +name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1 +def: "Standard medium confidence XCorr parameter for charge = 1." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001709 +name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2 +def: "Standard medium confidence XCorr parameter for charge = 2." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001710 +name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3 +def: "Standard medium confidence XCorr parameter for charge = 3." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001711 +name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4 +def: "Standard medium confidence XCorr parameter for charge >= 4." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001712 +name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1 +def: "FT high confidence XCorr parameter for charge = 1." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001713 +name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2 +def: "FT high confidence XCorr parameter for charge = 2." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001714 +name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3 +def: "FT high confidence XCorr parameter for charge = 3." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001715 +name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4 +def: "FT high confidence XCorr parameter for charge >= 4." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001716 +name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1 +def: "FT medium confidence XCorr parameter for charge = 1." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001717 +name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2 +def: "FT medium confidence XCorr parameter for charge = 2." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001718 +name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3 +def: "FT medium confidence XCorr parameter for charge = 3." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001719 +name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4 +def: "FT medium confidence XCorr parameter for charge >= 4." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001720 +name: ProteomeDiscoverer:1. Dynamic Modification +def: "OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter." [PSI:PI] +comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001721 +name: ProteomeDiscoverer:2. Dynamic Modification +def: "OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter." [PSI:PI] +comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001722 +name: ProteomeDiscoverer:3. Dynamic Modification +def: "OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter." [PSI:PI] +comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001723 +name: ProteomeDiscoverer:4. Dynamic Modification +def: "OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter." [PSI:PI] +comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001724 +name: ProteomeDiscoverer:Static Modification for X +def: "Static Modification for X." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001725 +name: ProteomeDiscoverer:Initial minimal peptide probability +def: "Minimal initial peptide probability to contribute to analysis." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001726 +name: ProteomeDiscoverer:Minimal peptide probability +def: "Minimum adjusted peptide probability contributing to protein probability." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001727 +name: ProteomeDiscoverer:Minimal peptide weight +def: "Minimum peptide weight contributing to protein probability." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001728 +name: ProteomeDiscoverer:Number of input1 spectra +def: "Number of spectra from 1+ precursor ions." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001729 +name: ProteomeDiscoverer:Number of input2 spectra +def: "Number of spectra from 2+ precursor ions." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001730 +name: ProteomeDiscoverer:Number of input3 spectra +def: "Number of spectra from 3+ precursor ions." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001731 +name: ProteomeDiscoverer:Number of input4 spectra +def: "Number of spectra from 4+ precursor ions." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001732 +name: ProteomeDiscoverer:Number of input5 spectra +def: "Number of spectra from 5+ precursor ions." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001733 +name: ProteomeDiscoverer:Number of predicted correct proteins +def: "Total number of predicted correct protein ids (sum of probabilities)." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001734 +name: ProteomeDiscoverer:Organism +def: "OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001735 +name: ProteomeDiscoverer:Reference Database +def: "OBSOLETE Full path database name." [PSI:MS] +comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001736 +name: ProteomeDiscoverer:Residue substitution list +def: "Residues considered equivalent when comparing peptides." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001737 +name: ProteomeDiscoverer:Source file extension +def: "OBSOLETE File type (if not pepXML)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001738 +name: ProteomeDiscoverer:Source Files +def: "OBSOLETE Input pepXML files." [PSI:MS] +comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001739 +name: ProteomeDiscoverer:Source Files old +def: "OBSOLETE Input pepXML files (old)." [PSI:MS] +comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001740 +name: ProteomeDiscoverer:WinCyg reference database +def: "Windows full path for database." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001741 +name: ProteomeDiscoverer:WinCyg source files +def: "Windows pepXML file names." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001742 +name: LTQ Orbitrap Velos +def: "Finnigan LTQ Orbitrap Velos MS." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1001743 +name: ProteomeDiscoverer:Mascot:Weight of A Ions +def: "Determines if to use A ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001744 +name: ProteomeDiscoverer:Mascot:Weight of B Ions +def: "Determines if to use B ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001745 +name: ProteomeDiscoverer:Mascot:Weight of C Ions +def: "Determines if to use C ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001746 +name: ProteomeDiscoverer:Mascot:Weight of D Ions +def: "Determines if to use D ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001747 +name: ProteomeDiscoverer:Mascot:Weight of V Ions +def: "Determines if to use V ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001748 +name: ProteomeDiscoverer:Mascot:Weight of W Ions +def: "Determines if to use W ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001749 +name: ProteomeDiscoverer:Mascot:Weight of X Ions +def: "Determines if to use X ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001750 +name: ProteomeDiscoverer:Mascot:Weight of Y Ions +def: "Determines if to use Y ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001751 +name: ProteomeDiscoverer:Mascot:Weight of Z Ions +def: "Determines if to use z ions for spectrum matching." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001752 +name: ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation +def: "Determines if to use precursor reevaluation." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001753 +name: ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly +def: "Signal-to-Noise ratio below which peaks are removed (in FT mode only)." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001754 +name: ProteomeDiscoverer:Mascot:Please Do not Touch this +def: "Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001755 +name: contact phone number +def: "Phone number of the contact person or organization." [PSI:MS] +is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001756 +name: contact fax number +def: "Fax number for the contact person or organization." [PSI:MS] +is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001757 +name: contact toll-free phone number +def: "Toll-free phone number of the contact person or organization." [PSI:MS] +is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001758 +name: Mascot:SigThresholdType +def: "Significance threshold type used in Mascot reporting (either 'identity' or 'homology')." [PSI:MS] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001759 +name: Mascot:ProteinGrouping +def: "Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering')." [PSI:MS] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001760 +name: Percolator:features +def: "List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'." [PSI:MS] +is_a: MS:1002107 ! Percolator input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001761 +name: ACQUITY UPLC +def: "Waters LC-system ACQUITY UPLC." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001762 +name: ACQUITY UPLC H-Class +def: "Waters LC-system ACQUITY UPLC H-Class." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001763 +name: ACQUITY UPLC H-Class Bio +def: "Waters LC-system ACQUITY UPLC H-Class Bio." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001764 +name: ACQUITY UPLC I-Class +def: "Waters LC-system ACQUITY UPLC I-Class." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001765 +name: ACQUITY UPLC Systems with 2D Technology +def: "Waters LC-system ACQUITY UPLC Systems with 2D Technology." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001766 +name: nanoACQUITY UPLC +def: "Waters LC-system nanoACQUITY UPLC." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001767 +name: nanoACQUITY UPLC System with 1D Technology +def: "Waters LC-system nanoACQUITY UPLC System with 1D Technology." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001768 +name: nanoACQUITY UPLC with HDX Technology +def: "Waters LC-system nanoACQUITY UPLC with HDX Technology." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001769 +name: TRIZAIC UPLC nanoTile +def: "Waters LC-system TRIZAIC UPLC nanoTile." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001770 +name: GCT Premier +def: "Waters oa-ToF based GCT Premier." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001771 +name: MALDI Synapt G2 HDMS +def: "Waters oa-ToF based MALDI Synapt G2 HDMS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001772 +name: MALDI Synapt G2 MS +def: "Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001773 +name: MALDI Synapt G2-S HDMS +def: "Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001774 +name: MALDI Synapt G2-S MS +def: "Waters oa-ToF based MALDI Synapt G2-S MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001775 +name: MALDI Synapt HDMS +def: "Waters oa-ToF based MALDI Synapt HDMS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001776 +name: MALDI Synapt MS +def: "Waters oa-ToF based MALDI Synapt MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001777 +name: Synapt G2 HDMS +def: "Waters oa-ToF based Synapt G2 HDMS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001778 +name: Synapt G2 MS +def: "Waters oa-ToF based Synapt G2 MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001779 +name: Synapt G2-S HDMS +def: "Waters oa-ToF based Synapt G2-S HDMS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001780 +name: Synapt G2-S MS +def: "Waters oa-ToF based Synapt G2-S MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001781 +name: Synapt HDMS +def: "Waters oa-ToF based Synapt HDMS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001782 +name: Synapt MS +def: "Waters oa-ToF based Synapt MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001783 +name: Xevo G2 Q-Tof +def: "Waters oa-ToF based Xevo G2 Q-Tof." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001784 +name: Xevo G2 Tof +def: "Waters oa-ToF based Xevo G2 Tof." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001785 +name: Xevo Q-Tof +def: "Waters oa-ToF based Xevo Q-Tof." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001786 +name: 3100 +def: "Waters quadrupole based 3100." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001787 +name: Acquity SQD +def: "Waters quadrupole based Acquity SQD." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001788 +name: Acquity TQD +def: "Waters quadrupole based Acquity TQD." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001789 +name: Quattro micro GC +def: "Waters (triple) quadrupole based Quattro micro GC." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001790 +name: Xevo TQ MS +def: "Waters quadrupole based Xevo TQ MS." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001791 +name: Xevo TQD +def: "Waters quadrupole based Xevo TQD." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001792 +name: Xevo TQ-S +def: "Waters quadrupole based Xevo TQ-S." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1001793 +name: Mascot:PreferredTaxonomy +def: "NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences." [PSI:MS] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001795 +name: Empower +def: "Waters Empower software for liquid chromatography and mass spectrometry acquisition." [PSI:MS] +is_a: MS:1000694 ! Waters software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001796 +name: UNIFY +def: "Waters UNIFY software for liquid chromatography and mass spectrometry acquisition." [PSI:MS] +is_a: MS:1000694 ! Waters software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001797 +name: travelling wave ion mobility mass spectrometer +def: "OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide." [PSI:MS] +comment: This child of the former purgatory term ion mobility spectrometry was made obsolete. +synonym: "TWIMS" EXACT [] +is_obsolete: true + +[Term] +id: MS:1001798 +name: LECO software +def: "LECO software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1001799 +name: ChromaTOF software +def: "Software for acquisition, processing and analysis of data for LECO instruments." [PSI:MS] +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software +is_a: MS:1001798 ! LECO software + +[Term] +id: MS:1001800 +name: LECO instrument model +def: "LECO instrument model." [PSI:MS] +is_a: MS:1000031 ! instrument model + +[Term] +id: MS:1001801 +name: Pegasus HRT +def: "LECO high resolution time-of-flight GC mass spectrometer." [PSI:MS] +is_a: MS:1001800 ! LECO instrument model + +[Term] +id: MS:1001802 +name: Citius HRT +def: "LECO high resolution time-of-flight LC mass spectrometer." [PSI:MS] +is_a: MS:1001800 ! LECO instrument model + +[Term] +id: MS:1001803 +name: Pegasus +def: "LECO GC time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1001800 ! LECO instrument model + +[Term] +id: MS:1001804 +name: TruTOF +def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1001800 ! LECO instrument model + +[Term] +id: MS:1001805 +name: quantification datatype +def: "The data type of the value reported in a QuantLayer." [PSI:MS] +is_a: MS:1001129 ! quantification information + +[Term] +id: MS:1001806 +name: quantification object attribute +def: "Attributes describing the details of an object relevant for reporting quantification workflows or values." [PSI:MS] +is_a: MS:1001129 ! quantification information + +[Term] +id: MS:1001807 +name: study variable attribute +def: "Attribute describing a study variable." [PSI:MS] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1001808 +name: technical replicate +def: "The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'." [PSI:MS] +is_a: MS:1001807 ! study variable attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001809 +name: biological replicate +def: "The study variable is 'biological replicate'. This means, the run was generated from another individual or sample." [PSI:MS] +is_a: MS:1001807 ! study variable attribute + +[Term] +id: MS:1001810 +name: experimental condition 'case' +def: "The experimental condition is 'case' in contrast to 'control'." [PSI:MS] +is_a: MS:1001807 ! study variable attribute + +[Term] +id: MS:1001811 +name: experimental condition 'control' +def: "The experimental condition is 'control' in contrast to 'case'." [PSI:MS] +is_a: MS:1001807 ! study variable attribute + +[Term] +id: MS:1001812 +name: experimental condition 'disease' +def: "The experimental condition is 'disease' in contrast to 'healthy'." [PSI:MS] +is_a: MS:1001807 ! study variable attribute + +[Term] +id: MS:1001813 +name: experimental condition 'healthy' +def: "The experimental condition is 'healthy' in contrast to 'disease'." [PSI:MS] +is_a: MS:1001807 ! study variable attribute + +[Term] +id: MS:1001814 +name: generic experimental condition +def: "The experimental condition is given in the value of this term." [PSI:MS] +is_a: MS:1001807 ! study variable attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001815 +name: time series, time point X +def: "The experimental design followed a time series design. The time point of this run is given in the value of this term." [PSI:MS] +is_a: MS:1001807 ! study variable attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001816 +name: dilution series, concentration X +def: "The experimental design followed a dilution series design. The concentration of this run is given in the value of this term." [PSI:MS] +is_a: MS:1001807 ! study variable attribute +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001817 +name: raw file attribute +def: "Attribute describing a raw file." [PSI:MS] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1001818 +name: one sample run +def: "The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free)." [PSI:MS] +is_a: MS:1001817 ! raw file attribute + +[Term] +id: MS:1001819 +name: two sample run +def: "The raw file contains the run of two samples (e.g. SILAC, metabolic labelling)." [PSI:MS] +is_a: MS:1001817 ! raw file attribute + +[Term] +id: MS:1001820 +name: three sample run +def: "The raw file contains the run of three samples (e.g. 3-plex SILAC)." [PSI:MS] +is_a: MS:1001817 ! raw file attribute + +[Term] +id: MS:1001821 +name: four sample run +def: "The raw file contains the run of four samples (e.g. 4-plex iTraq)." [PSI:MS] +is_a: MS:1001817 ! raw file attribute + +[Term] +id: MS:1001822 +name: eight sample run +def: "The raw file contains the run of eight samples (e.g. 8-plex iTraq)." [PSI:MS] +is_a: MS:1001817 ! raw file attribute + +[Term] +id: MS:1001823 +name: raw files group attribute +def: "Attribute describing, how raw files build a raw file group." [PSI:MS] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1001824 +name: merge of runs of 1D gel bands +def: "Attribute describing, how raw files build a raw file group." [PSI:MS] +is_a: MS:1001823 ! raw files group attribute + +[Term] +id: MS:1001825 +name: feature list attribute +def: "Attribute describing a feature list." [PSI:MS] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1001826 +name: mass trace reporting: rectangles +def: "The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given." [PSI:MS] +is_a: MS:1001825 ! feature list attribute + +[Term] +id: MS:1001827 +name: mass trace reporting: polygons +def: "The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit." [PSI:MS] +is_a: MS:1001825 ! feature list attribute + +[Term] +id: MS:1001828 +name: feature attribute +def: "Attribute describing a feature." [PSI:MS] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1001829 +name: SRM transition ID +def: "Identifier for an SRM transition in an external document describing additional information about the transition." [PSI:MS] +is_a: MS:1001828 ! feature attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001830 +name: Progenesis LC-MS +def: "Software from Nonlinear Dynamics for LC-MS label-free workflow." [PSI:MS] +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1001831 +name: SILACAnalyzer +def: "Software for SILAC workflow." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1001832 +name: quantitation software comment or customizations +def: "Quantitation software comment or any customizations to the default setup of the software." [PSI:PI] +is_a: MS:1001129 ! quantification information +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001833 +name: quantitation analysis summary +def: "The overall workflow of this quantitation report." [PSI:PI] +is_a: MS:1001129 ! quantification information + +[Term] +id: MS:1001834 +name: LC-MS label-free quantitation analysis +def: "LC-MS label-free workflow (RT m/z map)." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1001835 +name: SILAC quantitation analysis +def: "SILAC workflow (heavy, light, and sometimes medium peak)." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1001836 +name: spectral counting quantitation analysis +def: "Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant)." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1001837 +name: iTRAQ quantitation analysis +def: "Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range." [PSI:PI, PMID:15385600] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1001838 +name: SRM quantitation analysis +def: "Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair)." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1001839 +name: metabolic labeling 14N / 15N quantitation analysis +def: "Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens)." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1001840 +name: LC-MS feature intensity +def: "Maximum peak intensity of the LC-MS feature." [PSI:PI] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001841 +name: LC-MS feature volume +def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001842 +name: sequence-level spectral count +def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001843 +name: MS1 feature maximum intensity +def: "Maximum intensity of MS1 feature." [PSI:PI] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001844 +name: MS1 feature area +def: "Area of MS1 feature." [PSI:PI] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001845 +name: peak area +def: "OBSOLETE Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI] +comment: This term was made obsolete because it was a duplication of MS:1001844. +is_a: MS:1001805 ! quantification datatype +is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001846 +name: isotopic pattern area +def: "Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N)." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001847 +name: reporter ion intensity +def: "Intensity of MS2 reporter ion (e.g. iTraq)." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001848 +name: simple ratio of two values +def: "Simple ratio of two values (enumerator and denominator)." [PSI:PI] +is_a: MS:1002066 ! ratio calculation method + +[Term] +id: MS:1001849 +name: sum of MatchedFeature values +def: "OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI] +comment: This term was made obsolete because the concept MatchedFeature was dropped. +is_a: MS:1002735 ! feature-level quantification datatype +is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001850 +name: normalized peptide value +def: "Normalized peptide value." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001851 +name: protein value: sum of peptide values +def: "Protein quantification value calculated as sum of peptide values." [PSI:PI] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001852 +name: normalized protein value +def: "Normalized protein value." [PSI:PI] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001853 +name: max fold change +def: "Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis)." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001854 +name: ANOVA p-value +def: "Global datatype: p-value of ANOVA of group means (e.g. Progenesis)." [PSI:PI] +is_a: MS:1002072 ! p-value +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001855 +name: t-test p-value +def: "P-value of t-Test of two groups." [PSI:PI] +is_a: MS:1002072 ! p-value +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001856 +name: reporter ion raw value +def: "Intensity (or area) of MS2 reporter ion (e.g. iTraq)." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001857 +name: reporter ion normalized value +def: "Normalized value of MS2 reporter ion (e.g. iTraq)." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001858 +name: XIC area +def: "Area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001859 +name: normalized XIC area +def: "Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001860 +name: protein value: mean of peptide ratios +def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001861 +name: quantification data processing +def: "Terms used to describe types of quantification data processing." [PSI:MS] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1001862 +name: normalization to mean of sum of all proteins +def: "Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting)." [PSI:MS] +is_a: MS:1001861 ! quantification data processing + +[Term] +id: MS:1001863 +name: quantile normalization, proteins +def: "Normalization of protein values to approach the same distribution." [PSI:MS] +is_a: MS:1001861 ! quantification data processing + +[Term] +id: MS:1001864 +name: quantile normalization, peptides +def: "Normalization of peptide values to approach the same distribution." [PSI:MS] +is_a: MS:1001861 ! quantification data processing + +[Term] +id: MS:1001865 +name: Progenesis automatic alignment +def: "Automatic RT alignment of Progenesis software." [PSI:MS] +is_a: MS:1001861 ! quantification data processing + +[Term] +id: MS:1001866 +name: Progenesis manual alignment +def: "RT alignment of Progenesis software using automatic and manual vectors." [PSI:MS] +is_a: MS:1001861 ! quantification data processing + +[Term] +id: MS:1001867 +name: Progenesis normalization +def: "Normalization as performed by Progenesis LC-MS." [PSI:MS] +is_a: MS:1001861 ! quantification data processing + +[Term] +id: MS:1001868 +name: distinct peptide-level q-value +def: "Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [PSI:PI] +is_a: MS:1002484 ! peptide-level statistical threshold +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001869 +name: protein-level q-value +def: "Estimation of the q-value for proteins." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001870 +name: peptide sequence-level p-value +def: "Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001871 +name: protein-level p-value +def: "Estimation of the p-value for proteins." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001872 +name: peptide sequence-level e-value +def: "Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic +relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001873 +name: protein-level e-value +def: "Estimation of the e-value for proteins." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic +relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001874 +name: FDRScore +def: "OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0." [PMID:19253293] +comment: This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374). +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001875 +name: modification motif +def: "The regular expression describing the sequence motif for a modification." [PSI:PI] +is_a: MS:1001056 ! modification specificity rule +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001876 +name: modification probability +def: "The a priori probability of a modification." [PSI:PI] +is_a: MS:1001056 ! modification specificity rule + +[Term] +id: MS:1001877 +name: ChromaTOF HRT software +def: "Software for acquisition, processing and analysis of data for LECO instruments." [PSI:MS] +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software +is_a: MS:1001798 ! LECO software + +[Term] +id: MS:1001878 +name: MALDI Solutions Microbial Identification +def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS] +is_a: MS:1001558 ! MALDI Solutions + +[Term] +id: MS:1001879 +name: offset voltage +def: "The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation." [PSI:MS] +is_a: MS:1000482 ! source attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001880 +name: in-source collision-induced dissociation +def: "The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum." [PSI:MS] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1001881 +name: mz5 format +def: "mz5 file format, modelled after mzML." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1001882 +name: transition validation attribute +def: "Attributes of the quality of a transition that affect its selection as appropriate." [PSI:MS] +relationship: part_of MS:1000908 ! transition + +[Term] +id: MS:1001883 +name: coefficient of variation +def: "Variation of a set of signal measurements calculated as the standard deviation relative to the mean." [PSI:MS] +is_a: MS:1001882 ! transition validation attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001884 +name: signal-to-noise ratio +def: "Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal." [PSI:MS] +is_a: MS:1001882 ! transition validation attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001885 +name: command-line parameters +def: "Parameters string passed to a command-line interface software application, omitting the executable name." [PSI:MS] +is_a: MS:1000630 ! data processing parameter +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001886 +name: SQID +def: "Software for data analysis of peptides and proteins." [PSI:MS] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001887 +name: SQID:score +def: "The SQID result 'Score'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic + +[Term] +id: MS:1001888 +name: SQID:deltaScore +def: "The SQID result 'deltaScore'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic + +[Term] +id: MS:1001889 +name: SQID:protein score +def: "The SQID result 'protein score'." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins + +[Term] +id: MS:1001890 +name: Progenesis:protein normalised abundance +def: "The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001891 +name: Progenesis:peptide normalised abundance +def: "The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001892 +name: Progenesis:protein raw abundance +def: "The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001893 +name: Progenesis:peptide raw abundance +def: "The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001894 +name: Progenesis:confidence score +def: "The data type confidence score produced by Progenesis LC-MS." [PSI:MS] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001895 +name: Progenesis:peptide count +def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001896 +name: Progenesis:feature intensity +def: "The data type feature intensity produced by Progenesis LC-MS." [PSI:MS] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001897 +name: MaxQuant:peptide counts (unique) +def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001898 +name: MaxQuant:peptide counts (all) +def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001899 +name: MaxQuant:peptide counts (razor+unique) +def: "The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001900 +name: MaxQuant:sequence length +def: "The data type sequence length produced by MaxQuant." [PSI:MS] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001901 +name: MaxQuant:PEP +def: "The data type PEP (posterior error probability) produced by MaxQuant." [PSI:MS] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001902 +name: MaxQuant:LFQ intensity +def: "The data type LFQ intensity produced by MaxQuant." [PSI:MS] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001903 +name: MaxQuant:feature intensity +def: "The data type feature intensity produced by MaxQuant." [PSI:MS] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001904 +name: MaxQuant:MS/MS count +def: "The data type MS2 count produced by MaxQuant." [PSI:MS] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1001905 +name: emPAI value +def: "The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001906 +name: APEX value +def: "The APEX value of protein abundance, produced from the APEX software." [PSI:MS] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001907 +name: retention time window width +def: "The full width of a retention time window for a chromatographic peak." [PSI:MS] +is_a: MS:1000915 ! retention time window attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001908 +name: ISQ +def: "Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1001909 +name: Velos Plus +def: "Thermo Scientific second generation Velos." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1001910 +name: LTQ Orbitrap Elite +def: "Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1001911 +name: Q Exactive +def: "Thermo Scientific Q Exactive." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1001912 +name: PinPoint +def: "Thermo Scientific PinPoint SRM analysis software." [PSI:MS] +is_a: MS:1000693 ! Thermo Finnigan software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001913 +name: S-lens voltage +def: "Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts." [PSI:MS] +is_a: MS:1000482 ! source attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001914 +name: pymzML +def: "Python module to interface mzML Data." [PSI:MS] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001915 +name: leukocyte elastase +def: "Enzyme leukocyte elastase (EC 3.4.21.37)." [BRENDA:3.4.21.37] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001957 ! (?<=[ALIV])(?!P) + +[Term] +id: MS:1001916 +name: proline endopeptidase +def: "Enzyme proline endopeptidase (EC 3.4.21.26)." [BRENDA:3.4.21.26] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001958 ! (?<=[HKR]P)(?!P) + +[Term] +id: MS:1001917 +name: glutamyl endopeptidase +def: "Enzyme glutamyl endopeptidase (EC 3.4.21.19)." [BRENDA:3.4.21.19] +synonym: "staphylococcal protease" EXACT [] +synonym: "Glu-C" EXACT [] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001959 ! (?<=[^E]E) + +[Term] +id: MS:1001918 +name: 2-iodobenzoate +def: "Chemical iodobenzoate. Cleaves after W." [PubChem_Compound:4739928] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001960 ! (?<=W) + +[Term] +id: MS:1001919 +name: ProteomeXchange accession number +def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001921 +name: ProteomeXchange accession number version number +def: "Version number of a ProteomeXchange accession number." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001922 +name: Digital Object Identifier (DOI) +def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org] +synonym: "doi" EXACT [] +is_a: MS:1000878 ! external reference identifier +relationship: has_regexp MS:1002480 ! (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+) +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001923 +name: external reference keyword +def: "Free text attribute that can enrich the information about an entity." [PSI:PI] +is_a: MS:1002840 ! external reference data +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001924 +name: journal article keyword +def: "Keyword present in a scientific publication." [PSI:PI] +is_a: MS:1001923 ! external reference keyword +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001925 +name: submitter keyword +def: "Keyword assigned by the data submitter." [PSI:PI] +is_a: MS:1001923 ! external reference keyword +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001926 +name: curator keyword +def: "Keyword assigned by a data curator." [PSI:PI] +is_a: MS:1001923 ! external reference keyword +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001927 +name: Tranche file hash +def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001928 +name: Tranche project hash +def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001929 +name: PRIDE experiment URI +def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1001930 +name: PRIDE project URI +def: "URI that allows the access to one project in the PRIDE database." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1001931 +name: source interface +def: "The source interface." [PSI:MS] +relationship: part_of MS:1000458 ! source + +[Term] +id: MS:1001932 +name: source interface model +def: "The source interface model." [PSI:MS] +relationship: part_of MS:1001931 ! source interface +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001933 +name: source sprayer +def: "The source sprayer." [PSI:MS] +relationship: part_of MS:1000458 ! source +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001934 +name: source sprayer type +def: "The source sprayer type." [PSI:MS] +relationship: part_of MS:1001933 ! source sprayer + +[Term] +id: MS:1001935 +name: source sprayer manufacturer +def: "The source sprayer manufacturer." [PSI:MS] +relationship: part_of MS:1001933 ! source sprayer +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001936 +name: source sprayer model +def: "The source sprayer model." [PSI:MS] +relationship: part_of MS:1001933 ! source sprayer +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001937 +name: sample plate +def: "Plate where the sample solution is spotted in a MALDI or similar instrument." [PSI:MS] +relationship: part_of MS:1000458 ! source + +[Term] +id: MS:1001938 +name: sample plate type +def: "The sample plate type." [PSI:MS] +relationship: part_of MS:1001937 ! sample plate + +[Term] +id: MS:1001939 +name: stainless steel plate +def: "Stainless steel plate." [PSI:MS] +is_a: MS:1001938 ! sample plate type + +[Term] +id: MS:1001940 +name: coated glass plate +def: "Coated glass plate." [PSI:MS] +is_a: MS:1001938 ! sample plate type + +[Term] +id: MS:1001941 +name: electrospray supply type +def: "Whether the sprayer is fed or is loaded with sample once." [PSI:MS] +relationship: part_of MS:1000458 ! source + +[Term] +id: MS:1001942 +name: static supply electrospray +def: "The sprayer is loaded with sample once." [PSI:MS] +is_a: MS:1001941 ! electrospray supply type + +[Term] +id: MS:1001943 +name: fed supply electrospray +def: "The sprayer is continuously fed with sample." [PSI:MS] +is_a: MS:1001941 ! electrospray supply type + +[Term] +id: MS:1001944 +name: Collision cell exit potential +def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_units UO:0000218 ! volt +synonym: "CXP" EXACT [] +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001945 +name: Pegasus 4D +def: "LECO nominal mass resolution time-of-flight GCxGC mass spectrometer." [PSI:MS] +is_a: MS:1001800 ! LECO instrument model + +[Term] +id: MS:1001946 +name: PEAKS Studio +def: "PEAKS Studio software for data analysis." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001947 +name: PEAKS Online +def: "PEAKS Online software for high throughput data analysis." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001948 +name: PEAKS Node +def: "PEAKS Node software for high throughput data analysis." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1001949 +name: BSI software +def: "Bioinformatics Solutions Inc. Software for data processing and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1001950 +name: PEAKS:peptideScore +def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001951 +name: PEAKS:proteinScore +def: "The PEAKS protein '-10lgP Score'." [PSI:MS] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001952 +name: ZCore:probScore +def: "The ZCore probability score." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001953 +name: source interface manufacturer +def: "The source interface manufacturer." [PSI:MS] +relationship: part_of MS:1001931 ! source interface +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001954 +name: acquisition parameter +def: "Parameters used in the mass spectrometry acquisition." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001955 +name: no cleavage +def: "No cleavage." [PSI:MS] +is_a: MS:1001045 ! cleavage agent name + +[Term] +id: MS:1001956 +name: unspecific cleavage +def: "Unspecific cleavage." [PSI:MS] +is_a: MS:1001045 ! cleavage agent name + +[Term] +id: MS:1001957 +name: (?<=[ALIV])(?!P) +def: "Regular expression for leukocyte elastase." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001958 +name: (?<=[HKR]P)(?!P) +def: "Regular expression for proline endopeptidase." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001959 +name: (?<=[^E]E) +def: "Regular expression for glutamyl endopeptidase." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001960 +name: (?<=W) +def: "Regular expression for 2-iodobenzoate." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1001961 +name: peptide spectrum match scoring algorithm +def: "Algorithm used to score the match between a spectrum and a peptide ion." [PSI:MS] +relationship: part_of MS:1001458 ! spectrum generation information +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001962 +name: Mascot:C13 counts +def: "C13 peaks to use in peak detection." [PSI:MS] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1001963 +name: ProteinExtractor:Weighting +def: "Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS] +is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001964 +name: ProteinScape:second round Mascot +def: "Flag indicating a second round search with Mascot." [PSI:MS] +is_a: MS:1002100 ! ProteinScape input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001965 +name: ProteinScape:second round Phenyx +def: "Flag indicating a second round search with Phenyx." [PSI:MS] +is_a: MS:1002100 ! ProteinScape input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1001966 +name: product ion mobility +def: "The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry." [PSI:MS] +is_a: MS:1001221 ! product ion attribute + +[Term] +id: MS:1001967 +name: product ion drift time +def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS] +is_a: MS:1002222 ! SRM transition attribute +relationship: has_units UO:0000028 ! millisecond +comment: This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476). +is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1001968 +name: PTM localization PSM-level statistic +def: "Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level." [PSI:MS] +is_a: MS:1002689 ! PTM localization single result statistic + +[Term] +id: MS:1001969 +name: phosphoRS score +def: "phosphoRS score for PTM site location at the PSM-level." [DOI:10.1021/pr200611n, PMID:22073976] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001970 +name: phosphoRS sequence probability +def: "Probability that the respective isoform is correct." [DOI:10.1021/pr200611n, PMID:22073976] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001971 +name: phosphoRS site probability +def: "Estimate of the probability that the respective site is truly phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001972 +name: PTM scoring algorithm version +def: "Version of the post-translational modification scoring algorithm." [PSI:MS] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001973 +name: DeBunker +def: "DeBunker software." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001974 +name: DeBunker:score +def: "Score specific to DeBunker." [PSI:MS] +is_a: MS:1001968 ! PTM localization PSM-level statistic +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001975 +name: delta m/z +def: "The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value." [PSI:MS] +synonym: "m/z difference" EXACT [] +is_a: MS:1001405 ! spectrum identification result details +relationship: has_units UO:0000166 ! parts per notation unit +relationship: has_units UO:0000169 ! parts per million +relationship: has_units UO:0000187 ! percent +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001976 +name: delta M +def: "The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value." [PSI:MS] +synonym: "mass difference" EXACT [] +is_a: MS:1001405 ! spectrum identification result details +relationship: has_units UO:0000166 ! parts per notation unit +relationship: has_units UO:0000169 ! parts per million +relationship: has_units UO:0000187 ! percent +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1001977 +name: MSQuant +def: "MSQuant software." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001978 +name: MSQuant:PTM-score +def: "The PTM score from MSQuant software." [DOI:10.1021/pr900721e, PMID:19888749] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001979 +name: MaxQuant:PTM Score +def: "The PTM score from MaxQuant software." [PSI:MS] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001980 +name: MaxQuant:Phospho (STY) Probabilities +def: "The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001981 +name: MaxQuant:Phospho (STY) Score Diffs +def: "The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001982 +name: MaxQuant:P-site localization probability +def: "The P-site localization probability value from MaxQuant software." [PSI:MS] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001983 +name: MaxQuant:PTM Delta Score +def: "The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest)." [PSI:MS] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001984 +name: Ascore software +def: "Ascore software." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1001985 +name: Ascore +def: "A-score for PTM site location at the PSM-level." [DOI:10.1038/nbt1240, PMID:16964243] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001986 +name: H-Score +def: "H-Score for peptide phosphorylation site location." [DOI:10.1021/pr1006813, PMID:20836569] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1001987 +name: vacuum drying MALDI sample preparation +def: "Vacuum-drying MALDI sample preparation crystallization method." [PSI:MS] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1001988 +name: crushed crystal MALDI sample preparation +def: "Crushed-crystal MALDI sample preparation method." [PSI:MS] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1001989 +name: fast evaporation MALDI sample preparation +def: "Fast-evaporation MALDI sample preparation method." [DOI:10.1021/ac00091a044] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1001990 +name: overlayer MALDI sample preparation +def: "Overlayer method combining features of the crushed-crystal method and the fast-evaporation method." [PSI:MS] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1001991 +name: sandwich MALDI sample preparation +def: "Sandwich MALDI sample preparation method." [DOI:10.1002/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.3.CO;2-4] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1001992 +name: spin coating MALDI sample preparation +def: "Spin coating MALDI sample preparation method." [DOI:10.1021/cc0500710, PMID:16283807] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1001993 +name: quick and dirty MALDI sample preparation +def: "Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling." [PSI:MS] +is_a: MS:1000833 ! matrix application type + +[Term] +id: MS:1001994 +name: top hat baseline reduction +def: "Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'." [PSI:MS] +is_a: MS:1000593 ! baseline reduction + +[Term] +id: MS:1001995 +name: convex hull baseline reduction +def: "Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures." [PSI:MS] +is_a: MS:1000593 ! baseline reduction + +[Term] +id: MS:1001996 +name: median baseline reduction +def: "The spectrum that will be baseline subtracted is divided into a number of segments." [PSI:MS] +is_a: MS:1000593 ! baseline reduction + +[Term] +id: MS:1001997 +name: wavelet transformation smoothing +def: "The random noise is removed by using the undecimated wavelet transform." [DOI:10.1093/bioinformatics/btl355, PMID:16820428] +is_a: MS:1000592 ! smoothing + +[Term] +id: MS:1001998 +name: sophisticated numerical annotation procedure +def: "It searches for known patterns in the measured spectrum." [DOI:10.1021/ac951158i, PMID:21619291] +synonym: "SNAP" EXACT [] +is_a: MS:1000801 ! area peak picking + +[Term] +id: MS:1001999 +name: area normalization +def: "Normalization of areas below the curves." [PSI:MS] +is_a: MS:1001484 ! intensity normalization + +[Term] +id: MS:1002000 +name: LIFT +def: "A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID." [DOI:10.1007/s00216-003-2057-0 , PMID:12830354] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1002001 +name: MS1 label-based raw feature quantitation +def: "MS1 label-based raw feature quantitation." [PSI:PI] +is_a: MS:1002018 ! MS1 label-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002002 +name: MS1 label-based peptide level quantitation +def: "MS1 label-based peptide level quantitation." [PSI:PI] +is_a: MS:1002018 ! MS1 label-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002003 +name: MS1 label-based protein level quantitation +def: "MS1 label-based protein level quantitation." [PSI:PI] +is_a: MS:1002018 ! MS1 label-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002004 +name: MS1 label-based proteingroup level quantitation +def: "MS1 label-based proteingroup level quantitation." [PSI:PI] +is_a: MS:1002018 ! MS1 label-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002005 +name: iRT retention time normalization standard +def: "A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys." [DOI:10.1002/pmic.201100463, http://www.biognosys.ch/products/rt-kit.html] +is_a: MS:1000901 ! retention time normalization standard + +[Term] +id: MS:1002006 +name: SRM transition type +def: "The type of the transitions, e.g. target or decoy." [PSI:MS] +synonym: "MRM transition type" EXACT [] +relationship: part_of MS:1000908 ! transition + +[Term] +id: MS:1002007 +name: target SRM transition +def: "A transition used to target a specific compound that may be in the sample." [PSI:MS] +synonym: "target MRM transition" EXACT [] +is_a: MS:1002006 ! SRM transition type + +[Term] +id: MS:1002008 +name: decoy SRM transition +def: "A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows." [PSI:MS] +synonym: "decoy MRM transition" EXACT [] +is_a: MS:1002006 ! SRM transition type + +[Term] +id: MS:1002009 +name: isobaric label quantitation analysis +def: "Quantitation analysis using an isobaric labelling workflow." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1002010 +name: TMT quantitation analysis +def: "Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002011 +name: desorption electrospray ionization +def: "Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure." [DOI:10.1126/science.1104404, PMID:15486296] +synonym: "DESI" EXACT [] +is_a: MS:1000240 ! atmospheric pressure ionization + +[Term] +id: MS:1002012 +name: Mascot:PTM site assignment confidence +def: "Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score)." [http://www.matrixscience.com/help/pt_mods_help.html#SITE] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002013 +name: collision energy ramp start +def: "Collision energy at the start of the collision energy ramp." [PSI:PI] +is_a: MS:1000045 ! collision energy +relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002014 +name: collision energy ramp end +def: "Collision energy at the end of the collision energy ramp." [PSI:PI] +is_a: MS:1000045 ! collision energy +relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002015 +name: spectral count peptide level quantitation +def: "Spectral count peptide level quantitation." [PSI:PI] +is_a: MS:1001836 ! spectral counting quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002016 +name: spectral count protein level quantitation +def: "Spectral count protein level quantitation." [PSI:PI] +is_a: MS:1001836 ! spectral counting quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002017 +name: spectral count proteingroup level quantitation +def: "Spectral count proteingroup level quantitation." [PSI:PI] +is_a: MS:1001836 ! spectral counting quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002018 +name: MS1 label-based analysis +def: "MS1 label-based analysis." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1002019 +name: label-free raw feature quantitation +def: "Label-free raw feature quantitation." [PSI:PI] +is_a: MS:1001834 ! LC-MS label-free quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002020 +name: label-free peptide level quantitation +def: "Label-free peptide level quantitation." [PSI:PI] +is_a: MS:1001834 ! LC-MS label-free quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002021 +name: label-free protein level quantitation +def: "Label-free protein level quantitation." [PSI:PI] +is_a: MS:1001834 ! LC-MS label-free quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002022 +name: label-free proteingroup level quantitation +def: "Label-free proteingroup level quantitation." [PSI:PI] +is_a: MS:1001834 ! LC-MS label-free quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002023 +name: MS2 tag-based analysis +def: "MS2 tag-based analysis." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1002024 +name: MS2 tag-based feature level quantitation +def: "MS2 tag-based feature level quantitation." [PSI:PI] +is_a: MS:1002023 ! MS2 tag-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002025 +name: MS2 tag-based peptide level quantitation +def: "MS2 tag-based peptide level quantitation." [PSI:PI] +is_a: MS:1002023 ! MS2 tag-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002026 +name: MS2 tag-based protein level quantitation +def: "MS2 tag-based protein level quantitation." [PSI:PI] +is_a: MS:1002023 ! MS2 tag-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002027 +name: MS2 tag-based proteingroup level quantitation +def: "MS2 tag-based proteingroup level quantitation." [PSI:PI] +is_a: MS:1002023 ! MS2 tag-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002028 +name: nucleic acid base modification +def: "Nucleic acid base modification (substitution, insertion or deletion)." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002029 +name: original nucleic acid sequence +def: "Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002030 +name: modified nucleic acid sequence +def: "Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002031 +name: PASSEL transition group browser URI +def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002032 +name: PeptideAtlas dataset URI +def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002033 +name: contact role +def: "Role of the contact person." [PSI:PI] +is_a: MS:1000585 ! contact attribute + +[Term] +id: MS:1002034 +name: first author +def: "The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution." [PSI:MS] +is_a: MS:1002033 ! contact role + +[Term] +id: MS:1002035 +name: senior author +def: "The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution." [PSI:MS] +is_a: MS:1002033 ! contact role + +[Term] +id: MS:1002036 +name: co-author +def: "One of a set of authors associated with a publication or release." [PSI:MS] +is_a: MS:1002033 ! contact role + +[Term] +id: MS:1002037 +name: dataset submitter +def: "A person who submits a dataset to a repository." [PSI:MS] +is_a: MS:1002033 ! contact role + +[Term] +id: MS:1002038 +name: label free sample +def: "A sample that has not been labelled or modified. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI] +synonym: "light sample" EXACT [] +is_a: MS:1000548 ! sample attribute + +[Term] +id: MS:1002039 +name: inlet attribute +def: "Inlet properties that are associated with a value." [PSI:MS] +is_a: MS:1000547 ! object attribute +relationship: part_of MS:1000458 ! source + +[Term] +id: MS:1002040 +name: inlet temperature +def: "The temperature of the inlet of a mass spectrometer." [PSI:MS] +is_a: MS:1000482 ! source attribute +is_a: MS:1002039 ! inlet attribute +relationship: has_units UO:0000012 ! kelvin +relationship: has_units UO:0000027 ! degree Celsius +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002041 +name: source temperature +def: "The temperature of the source of a mass spectrometer." [PSI:MS] +is_a: MS:1000482 ! source attribute +relationship: has_units UO:0000012 ! kelvin +relationship: has_units UO:0000027 ! degree Celsius +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002042 +name: modulation time +def: "The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column." [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429] +is_a: MS:1000857 ! run attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002043 +name: ProteinProspector +def: "ProteinProspector software for data acquisition and analysis." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002044 +name: ProteinProspector:score +def: "The ProteinProspector result 'Score'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002045 +name: ProteinProspector:expectation value +def: "The ProteinProspector result 'Expectation value'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002046 +name: native source path +def: "The original source path used for directory-based sources." [PSI:MS] +is_a: MS:1001458 ! spectrum generation information +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002047 +name: MS-GF +def: "MS-GF software used to re-score the peptide-spectrum matches." [DOI:10.1074/mcp.M110.003731, PMID:20829449] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002048 +name: MS-GF+ +synonym: "MS-GFDB" EXACT [] +def: "MS-GF+ software used to analyze the spectra." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002049 +name: MS-GF:RawScore +def: "MS-GF raw score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002050 +name: MS-GF:DeNovoScore +def: "MS-GF de novo score." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002051 +name: MS-GF:Energy +def: "MS-GF energy score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002052 +name: MS-GF:SpecEValue +def: "MS-GF spectral E-value." [PSI:PI] +is_a: MS:1002353 ! PSM-level e-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002053 +name: MS-GF:EValue +def: "MS-GF E-value." [PSI:PI] +is_a: MS:1002353 ! PSM-level e-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002054 +name: MS-GF:QValue +def: "MS-GF Q-value." [PSI:PI] +is_a: MS:1002354 ! PSM-level q-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002055 +name: MS-GF:PepQValue +def: "MS-GF peptide-level Q-value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002056 +name: MS-GF:PEP +def: "MS-GF posterior error probability." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002057 +name: modification specificity protein N-term +def: "As parameter for search engine: apply the modification only at the N-terminus of a protein." [PSI:PI] +is_a: MS:1001056 ! modification specificity rule + +[Term] +id: MS:1002058 +name: modification specificity protein C-term +def: "As parameter for search engine: apply the modification only at the C-terminus of a protein." [PSI:PI] +is_a: MS:1001056 ! modification specificity rule + +[Term] +id: MS:1002059 +name: Microsoft Excel +def: "Microsoft Excel (can be used for spectral counting)." [PSI:PI] +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1002060 +name: database UniProtKB/TrEMBL +def: "The name of the UniProtKB/TrEMBL database." [PSI:PI] +is_a: MS:1002126 ! database UniProtKB + +[Term] +id: MS:1002061 +name: decoy DB from UniProtKB/TrEMBL +def: "OBSOLETE Decoy database from a TrEMBL protein sequence database." [PSI:PI] +comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. +is_obsolete: true + +[Term] +id: MS:1002062 +name: metabolic labelling: natural N (mainly 14N) +def: "Metabolic labelling: natural N (mainly 14N)." [PSI:PI] +is_a: MS:1001055 ! modification parameters + +[Term] +id: MS:1002063 +name: FindPairs +def: "Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite." [http://www.medizinisches-proteom-center.de/software] +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1002064 +name: peptide consensus RT +def: "Peptide consensus retention time." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002065 +name: peptide consensus m/z +def: "Peptide consensus mass/charge ratio." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002066 +name: ratio calculation method +def: "Method used to calculate the ratio." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002067 +name: protein value: median of peptide ratios +def: "Protein quantification value calculated as median of peptide ratios." [PSI:PI] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002068 +name: metabolic labelling: heavy N (mainly 15N) +def: "Metabolic labelling: heavy N (mainly 15N)." [PSI:PI] +is_a: MS:1001055 ! modification parameters + +[Term] +id: MS:1002069 +name: metabolic labelling purity +def: "Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape." [PSI:PI] +is_a: MS:1001055 ! modification parameters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002070 +name: t-test +def: "Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed." [PSI:PI] +is_a: MS:1001861 ! quantification data processing +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002071 +name: ANOVA-test +def: "Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed." [PSI:PI] +is_a: MS:1001861 ! quantification data processing +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002072 +name: p-value +def: "P-value as result of one of the processing steps described. Specify in the description, which processing step it was." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002073 +name: mzIdentML format +def: "The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'." [PSI:PI, http://www.psidev.info/mzidentml] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1002074 +name: quantification file format +def: "File format containing quantification results." [PSI:PI] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1002075 +name: mzQuantML format +def: "The mzQuantML format for quantification data from the PSI. File extension '.mzq'." [PSI:PI, http://www.psidev.info/mzquantml] +is_a: MS:1002074 ! quantification file format + +[Term] +id: MS:1002076 +name: PAnalyzer +def: "PAnalyzer software for getting protein evidence categories." [http://code.google.com/p/ehu-bio/wiki/PAnalyzer] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002077 +name: impact +def: "Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1002078 +name: ProteomeDiscoverer:1. Static Modification +def: "OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter." [PSI:PI] +comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002079 +name: ProteomeDiscoverer:2. Static Modification +def: "OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter." [PSI:PI] +comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002080 +name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before +def: "Precursor clipping range before." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002081 +name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After +def: "Precursor clipping range after." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002082 +name: first column elution time +def: "The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002083 +name: second column elution time +def: "The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column." [PSI:MS] +is_a: MS:1000503 ! scan attribute +relationship: has_units UO:0000010 ! second +relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002084 +name: multidimensional chromatography modulation description +def: "Multidimensional chromatography modulation description." [PSI:MS] +is_a: MS:1000857 ! run attribute + +[Term] +id: MS:1002085 +name: two-dimensional gas chromatography with fixed modulation time +def: "Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition." [PSI:MS] +is_a: MS:1002084 ! multidimensional chromatography modulation description + +[Term] +id: MS:1002086 +name: two-dimensional gas chromatography with discrete modulation time steps +def: "Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time." [PSI:MS] +is_a: MS:1002084 ! multidimensional chromatography modulation description + +[Term] +id: MS:1002087 +name: two-dimensional liquid chromatography with fixed modulation time +def: "Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition." [PSI:MS] +is_a: MS:1002084 ! multidimensional chromatography modulation description + +[Term] +id: MS:1002088 +name: two-dimensional liquid chromatography with discrete modulation time steps +def: "Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time." [PSI:MS] +is_a: MS:1002084 ! multidimensional chromatography modulation description + +[Term] +id: MS:1002089 +name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold +def: "XCorr threshold for storing peptides that do not belong to a protein." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002090 +name: Calculate Probability Scores +def: "Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated." [PSI:MS] +is_a: MS:1002094 ! common search engine input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002091 +name: ProteomeDiscoverer:Maximum Delta Cn +def: "Delta Cn threshold for filtering out PSM's." [PSI:MS] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002092 +name: Percolator:Validation based on +def: "Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator." [PSI:MS] +is_a: MS:1002107 ! Percolator input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002093 +name: search engine input parameter +def: "Search engine input parameter." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1002094 +name: common search engine input parameter +def: "Search engine input parameter that is shared by more than one search engine." [PSI:PI] +is_a: MS:1002093 ! search engine input parameter + +[Term] +id: MS:1002095 +name: Mascot input parameter +def: "Search engine input parameters specific to Mascot." [PSI:PI, source:http://www.matrixscience.com/help/search_field_help.html] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002096 +name: SEQUEST input parameter +def: "Search engine input parameters specific to SEQUEST." [PSI:PI, source:http://fields.scripps.edu/sequest/parameters.html] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002097 +name: Phenyx input parameter +def: "Search engine input parameters specific to Phenyx." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002098 +name: ProteinExtractor input parameter +def: "Search engine input parameters specific to ProteinExtractor." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002099 +name: OMSSA input parameter +def: "Search engine input parameters specific to OMSSA." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002100 +name: ProteinScape input parameter +def: "Search engine input parameters specific to ProteinScape." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002101 +name: ProteomeDiscoverer input parameter +def: "Search engine input parameters specific to ProteomeDiscoverer." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002103 +name: software input parameter +def: "Software input parameters." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1002104 +name: common software input parameter +def: "Software input parameter that is shared by more than one software." [PSI:PI] +is_a: MS:1002103 ! software input parameter + +[Term] +id: MS:1002105 +name: software specific input parameter +def: "Software specific input parameter." [PSI:PI] +is_a: MS:1002103 ! software input parameter + +[Term] +id: MS:1002106 +name: Scaffold input parameter +def: "Search engine input parameters specific to Scaffold." [PSI:PI] +is_a: MS:1002105 ! software specific input parameter + +[Term] +id: MS:1002107 +name: Percolator input parameter +def: "Search engine input parameters specific to Percolator." [PSI:PI] +is_a: MS:1002105 ! software specific input parameter + +[Term] +id: MS:1002108 +name: higher score better +def: "Indicates that a higher score is better." [PSI:PI] +relationship: part_of MS:1001153 ! search engine specific score + +[Term] +id: MS:1002109 +name: lower score better +def: "Indicates that a lower score is better." [PSI:PI] +relationship: part_of MS:1001153 ! search engine specific score + +[Term] +id: MS:1002110 +name: assay attribute +def: "Attribute describing an assay." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002111 +name: assay label attribute +def: "Attribute describing an assay label." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002112 +name: protein group list attribute +def: "Attribute describing a protein group list." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002113 +name: protein group attribute +def: "Attribute describing a protein group." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002114 +name: protein list attribute +def: "Attribute describing a protein list." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002115 +name: peptide consensus list attribute +def: "Attribute describing a peptide consensus list." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002116 +name: peptide consensus attribute +def: "Attribute describing a peptide consensus." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002117 +name: small molecule list attribute +def: "Attribute describing a small molecule list." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002118 +name: small molecule attribute +def: "Attribute describing a small molecule." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002119 +name: small molecule modification attribute +def: "Attribute describing a small molecule modification." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002120 +name: experiment name +def: "The name for identifying an experiment." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002121 +name: spectral count feature +def: "Dummy decribing a spectral count feature." [PSI:PI] +is_a: MS:1001828 ! feature attribute + +[Term] +id: MS:1002122 +name: counts reporting +def: "FeatureList of spectral counts." [PSI:PI] +is_a: MS:1001825 ! feature list attribute + +[Term] +id: MS:1002123 +name: x-Tracker +def: "X-Tracker generic tool for quantitative proteomics." [https://bessantlab.org/software/x-tracker/] +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1002124 +name: ProteoSuite +def: "ProteoSuite software for the analysis of quantitative proteomics data." [DOI:10.1089/omi.2012.0022, PMID:22804616, http://www.proteosuite.org/] +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1002125 +name: combined FDRScore +def: "OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] +comment: This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375). +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002126 +name: database UniProtKB +def: "The name of the UniProtKB knowledgebase." [PSI:PI] +is_a: MS:1001013 ! database name + +[Term] +id: MS:1002127 +name: identification file attribute +def: "Attribute describing an identification file." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002128 +name: method file format +def: "Attribute describing a method file format." [PSI:PI] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1002129 +name: ITRAQAnalyzer +def: "Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment." [http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP__ITRAQAnalyzer.html] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002130 +name: identification file format +def: "Attribute describing an identification file format." [PSI:PI] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1002131 +name: TOPP noise filter +def: "Noise filter component of the TOPP software." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002132 +name: TOPP NoiseFilterGaussian +def: "Removes noise from profile spectra by using a gaussian smoothing." [PSI:PI] +is_a: MS:1002131 ! TOPP noise filter + +[Term] +id: MS:1002133 +name: TOPP NoiseFilterSGolay +def: "Removes noise from profile spectra by using a Savitzky-Golay smoothing." [PSI:PI] +is_a: MS:1002131 ! TOPP noise filter + +[Term] +id: MS:1002134 +name: TOPP peak picker +def: "Peak picker component of the TOPP software." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002135 +name: TOPP PeakPickerHiRes +def: "Finds mass spectrometric peaks in high-resoluted profile mass spectra." [PSI:PI] +is_a: MS:1002134 ! TOPP peak picker + +[Term] +id: MS:1002136 +name: TOPP PeakPickerWavelet +def: "Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra." [PSI:PI] +is_a: MS:1002134 ! TOPP peak picker + +[Term] +id: MS:1002137 +name: TOPP spectra filter +def: "Spectra filter component of the TOPP software." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002138 +name: TOPP SpectraFilterBernNorm +def: "Applies a Bern et al normalization to peak spectra." [PMID:15262780, DOI:10.1093/bioinformatics/bth947] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002139 +name: TOPP SpectraFilterMarkerMower +def: "Applies a filter to peak spectra for marked peaks." [PSI:PI] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002140 +name: TOPP SpectraFilterNLargest +def: "Retains the n largest peaks of a peak spectra." [PSI:PI] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002141 +name: TOPP SpectraFilterNormalizer +def: "Applies a TIC/maximal intensity normalization to peak spectra." [PSI:PI] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002142 +name: TOPP SpectraFilterParentPeakMower +def: "Filters putative unfragmented precursor ions from tandem spectra." [PSI:PI] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002143 +name: TOPP SpectraFilterScaler +def: "Applies a filter to peak spectra after intensity scaling according to rank." [PSI:PI] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002144 +name: TOPP SpectraFilterSqrtMower +def: "Applies a filter to peak spectra after intensity scaling to the square root." [PSI:PI] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002145 +name: TOPP SpectraFilterThresholdMower +def: "Applies a filter of peaks below a given threshold to peak spectra." [PSI:PI] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002146 +name: TOPP SpectraFilterWindowMower +def: "Applies a filter of the largest peaks in a sliding window over a peak spectrum." [PSI:PI] +is_a: MS:1002137 ! TOPP spectra filter + +[Term] +id: MS:1002147 +name: TOPP map aligner +def: "Map aligner component of the TOPP software." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002148 +name: TOPP MapAlignerIdentification +def: "Corrects retention time distortions between maps based on common peptide identifications." [PSI:PI] +is_a: MS:1002147 ! TOPP map aligner + +[Term] +id: MS:1002149 +name: TOPP MapAlignerPoseClustering +def: "Corrects retention time distortions between maps using a pose clustering approach." [PSI:PI] +is_a: MS:1002147 ! TOPP map aligner + +[Term] +id: MS:1002150 +name: TOPP MapAlignerSpectrum +def: "Corrects retention time distortions between maps by spectrum alignment." [PSI:PI] +is_a: MS:1002147 ! TOPP map aligner + +[Term] +id: MS:1002151 +name: numerator data type attribute +def: "Attribute describing the data type of the numerator of a ratio." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002152 +name: denominator data type attribute +def: "Attribute describing the data type of the denominator of a ratio." [PSI:PI] +is_a: MS:1001806 ! quantification object attribute + +[Term] +id: MS:1002153 +name: protein level PSM counts +def: "The number of spectra identified for this protein in spectral counting." [PSI:PI] +is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002154 +name: TOPP DTAExtractor +def: "Extracts spectra of an MS run file to several files in DTA format." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002155 +name: TOPP IDMerger +def: "Merges several protein/peptide identification files into one file." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002156 +name: TOPP IDFileConverter +def: "Converts identification engine file formats." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002157 +name: TOPP SpectraMerger +def: "Merges spectra from an LC/MS map, either by precursor or by RT blocks." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002158 +name: TOPP MzTabExporter +def: "Exports various XML formats to an mzTab file." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002159 +name: TOPP MassTraceExtractor +def: "Annotates mass traces in centroided LC/MS maps." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002160 +name: TOPP PrecursorMassCorrector +def: "Correct the precursor entries of tandem MS scans." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002161 +name: TOPP HighResPrecursorMassCorrector +def: "Performs precursor mz correction on centroided high resolution data." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002162 +name: TOPP AdditiveSeries +def: "Computes an additive series to quantify a peptide in a set of samples." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002163 +name: TOPP Decharger +def: "Decharges and merges different feature charge variants of the same chemical entity." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002164 +name: TOPP EICExtractor +def: "Quantifies signals at given positions in (raw or picked) LC/MS maps." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002165 +name: TOPP feature finder +def: "Feature finder component of the TOPP software." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002166 +name: TOPP FeatureFinderCentroided +def: "Detects two-dimensional features in centroided LC-MS data." [PSI:PI] +is_a: MS:1002165 ! TOPP feature finder + +[Term] +id: MS:1002167 +name: TOPP FeatureFinderRaw +def: "Detects two-dimensional features in uncentroided LC-MS data." [PSI:PI] +is_a: MS:1002165 ! TOPP feature finder + +[Term] +id: MS:1002168 +name: TOPP FeatureFinderIsotopeWavelet +def: "Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm." [PSI:PI] +is_a: MS:1002165 ! TOPP feature finder + +[Term] +id: MS:1002169 +name: TOPP FeatureFinderMetabo +def: "Detects two-dimensional features in centroided LC-MS data of metabolites." [PSI:PI] +is_a: MS:1002165 ! TOPP feature finder + +[Term] +id: MS:1002170 +name: TOPP FeatureFinderMRM +def: "Quantifies features LC-MS/MS MRM data." [PSI:PI] +is_a: MS:1002165 ! TOPP feature finder + +[Term] +id: MS:1002171 +name: TOPP ProteinQuantifier +def: "Computes protein abundances from annotated feature/consensus maps." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002172 +name: TOPP ConsensusMapNormalizer +def: "Normalizes maps of one consensus XML file (after linking)." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002173 +name: TOPP MapRTTransformer +def: "Applies retention time transformations to maps." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002174 +name: TOPP feature linker +def: "Feature linker component of the TOPP software." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002175 +name: TOPP FeatureLinkerLabeled +def: "Groups corresponding isotope-labeled features in a feature map." [PSI:PI] +is_a: MS:1002174 ! TOPP feature linker + +[Term] +id: MS:1002176 +name: TOPP FeatureLinkerUnlabeled +def: "Groups corresponding features from multiple maps." [PSI:PI] +is_a: MS:1002174 ! TOPP feature linker + +[Term] +id: MS:1002177 +name: TOPP FeatureLinkerUnlabeledQT +def: "Groups corresponding features from multiple maps using a quality threshold clustering approach." [PSI:PI] +is_a: MS:1002174 ! TOPP feature linker + +[Term] +id: MS:1002178 +name: TOPP CompNovo +def: "Performs a peptide/protein identification with the CompNovo engine." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002179 +name: TOPP CompNovoCID +def: "Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002180 +name: TOPP software adaptor +def: "Software adaptor to an external program in the TOPP software." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002181 +name: TOPP InspectAdapter +def: "Identifies MS2 spectra using the external program Inspect." [PSI:PI] +is_a: MS:1002180 ! TOPP software adaptor + +[Term] +id: MS:1002182 +name: TOPP MascotAdapter +def: "Identifies MS2 spectra using the external program Mascot." [PSI:PI] +is_a: MS:1002180 ! TOPP software adaptor + +[Term] +id: MS:1002183 +name: TOPP MascotAdapterOnline +def: "Identifies MS2 spectra using the online version of the external program Mascot." [PSI:PI] +is_a: MS:1002180 ! TOPP software adaptor + +[Term] +id: MS:1002184 +name: TOPP OMSSAAdapter +def: "Identifies MS2 spectra using the external program OMSSA." [PSI:PI] +is_a: MS:1002180 ! TOPP software adaptor + +[Term] +id: MS:1002185 +name: TOPP PepNovoAdapter +def: "Identifies MS2 spectra using the external program PepNovo." [PSI:PI] +is_a: MS:1002180 ! TOPP software adaptor + +[Term] +id: MS:1002186 +name: TOPP XTandemAdapter +def: "Identifies MS2 spectra using the external program XTandem." [PSI:PI] +is_a: MS:1002180 ! TOPP software adaptor + +[Term] +id: MS:1002187 +name: TOPP SpecLibSearcher +def: "Identifies peptide MS2 spectra by spectral matching with a searchable spectral library." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002188 +name: TOPP ConsensusID +def: "Computes a consensus identification from peptide identifications of several identification engines." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002189 +name: TOPP IDConflictResolver +def: "Resolves ambiguous annotations of features with peptide identifications." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002190 +name: TOPP IDFilter +def: "Filters results from protein or peptide identification engines based on different criteria." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002191 +name: TOPP IDMapper +def: "Assigns protein/peptide identifications to feature or consensus features." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002192 +name: TOPP IDPosteriorErrorProbability +def: "Estimates posterior error probabilities using a mixture model." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002193 +name: TOPP IDRTCalibration +def: "Calibrate Retention times of peptide hits to standards." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002194 +name: TOPP PeptideIndexer +def: "Refreshes the protein references for all peptide hits." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002195 +name: TOPP PrecursorIonSelector +def: "A tool for precursor ion selection based on identification results." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002196 +name: TOPP MRMMapper +def: "MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002197 +name: TOPP OpenSwath component +def: "OpenSwath component of the TOPP software." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002198 +name: TOPP OpenSwathAnalyzer +def: "Picks peaks and finds features in an SRM experiment." [PSI:PI] +is_a: MS:1002197 ! TOPP OpenSwath component + +[Term] +id: MS:1002199 +name: TOPP OpenSwathChromatogramExtractor +def: "Extract chromatograms (XIC) from a MS2 map file." [PSI:PI] +is_a: MS:1002197 ! TOPP OpenSwath component + +[Term] +id: MS:1002200 +name: TOPP OpenSwathDecoyGenerator +def: "Generates decoys according to different models for a specific TraML." [PSI:PI] +is_a: MS:1002197 ! TOPP OpenSwath component + +[Term] +id: MS:1002201 +name: TOPP OpenSwathFeatureXMLToTSV +def: "Converts a featureXML to a mProphet tsv (tab separated values)." [PSI:PI] +is_a: MS:1002197 ! TOPP OpenSwath component + +[Term] +id: MS:1002202 +name: TOPP OpenSwathRTNormalizer +def: "Generates a transformation file for retention time space into normalized space." [PSI:PI] +is_a: MS:1002197 ! TOPP OpenSwath component + +[Term] +id: MS:1002203 +name: TOPP ProteinInference +def: "Infer proteins from a list of (high-confidence) peptides." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002204 +name: TOPP FalseDiscoveryRate +def: "Estimates the false discovery rate on peptide and protein level using decoy searches." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002205 +name: ProteoWizard msconvert +def: "Converts, filters, and processes mass spectrometry data in variety of formats." [PSI:MS] +is_a: MS:1000615 ! ProteoWizard software + +[Term] +id: MS:1002206 +name: ProteoWizard idconvert +def: "Converts, filters, and processes identifications from shotgun proteomics experiments." [PSI:MS] +is_a: MS:1000615 ! ProteoWizard software + +[Term] +id: MS:1002207 +name: ProteoWizard chainsaw +def: "Filters and processes protein sequence databases." [PSI:MS] +is_a: MS:1000615 ! ProteoWizard software + +[Term] +id: MS:1002208 +name: ProteoWizard msaccess +def: "Filters, processes, and displays mass spectrometry data in a variety of ways." [PSI:MS] +is_a: MS:1000615 ! ProteoWizard software + +[Term] +id: MS:1002209 +name: ProteoWizard SeeMS +def: "An interactive GUI application to view and filter mass spectrometry data in a variety of formats." [PSI:MS] +is_a: MS:1000615 ! ProteoWizard software + +[Term] +id: MS:1002210 +name: IsobariQ +def: "A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data." [PMID:21067241, DOI:10.1021/pr1009977, http://folk.uio.no/magnusar/isobariq] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002211 +name: Variance stabilizing normalization +def: "The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation." [PMID:16646781] +is_a: MS:1001861 ! quantification data processing + +[Term] +id: MS:1002212 +name: IPTL quantitation analysis +def: "Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric." [PSI:PI, PMID:19655813] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002213 +name: PAnalyzer:conclusive protein +def: "A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] +is_a: MS:1001600 ! protein inference confidence category +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002214 +name: PAnalyzer:indistinguishable protein +def: "A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] +is_a: MS:1001600 ! protein inference confidence category +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002215 +name: PAnalyzer:non-conclusive protein +def: "A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] +is_a: MS:1001600 ! protein inference confidence category +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002216 +name: PAnalyzer:ambiguous group member +def: "A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] +is_a: MS:1001600 ! protein inference confidence category +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002217 +name: decoy peptide +def: "A putative identified peptide issued from a decoy sequence database." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002218 +name: percent collision energy ramp start +def: "Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] +is_a: MS:1000138 ! normalized collision energy +relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002219 +name: percent collision energy ramp end +def: "Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] +is_a: MS:1000138 ! normalized collision energy +relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002220 +name: MRMaid +def: "A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database." [PSI:PI] +is_a: MS:1000871 ! SRM software + +[Term] +id: MS:1002221 +name: MRMaid:peptide score +def: "Score in MRMaid to indicate the expected performance of the peptide in SRM." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +is_a: MS:1002363 ! search engine specific score for proteins + +[Term] +id: MS:1002222 +name: SRM transition attribute +def: "Attribute associated with a SRM transition." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +relationship: part_of MS:1000908 ! transition + +[Term] +id: MS:1002223 +name: precursor ion detection probability +def: "Probability of detecting precursor when parent protein is present." [PSI:PI] +is_a: MS:1002222 ! SRM transition attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002224 +name: product ion detection probability +def: "Probability of detecting product ion when precursor ion is present." [PSI:PI] +is_a: MS:1002222 ! SRM transition attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002225 +name: average product ion intensity +def: "Average value of product ion intensity in a collection of identified spectra." [PSI:PI] +is_a: MS:1001226 ! product ion intensity +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 + +[Term] +id: MS:1002226 +name: product ion intensity standard deviation +def: "Standard deviation of product ion intensity in a collection of identified spectra." [PSI:PI] +is_a: MS:1001226 ! product ion intensity +relationship: has_units MS:1000131 ! number of detector counts +relationship: has_units MS:1000132 ! percent of base peak +relationship: has_units MS:1000814 ! counts per second +relationship: has_units MS:1000905 ! percent of base peak times 100 + +[Term] +id: MS:1002227 +name: number of product ion observations +def: "The number of times the specific product ion has been observed in a series of SRM experiments." [PSI:PI] +is_a: MS:1002222 ! SRM transition attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002228 +name: number of precursor ion observations +def: "The number of times the specific precursor ion has been observed in a series of SRM experiments." [PSI:PI] +is_a: MS:1002222 ! SRM transition attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002229 +name: ProteomeDiscoverer:Mascot:Significance Middle +def: "Calculated relaxed significance when performing a decoy search for high-confidence peptides." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002230 +name: ProteomeDiscoverer:Mascot:Significance High +def: "Calculated relaxed significance when performing a decoy search for medium-confidence peptides." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002231 +name: regular expressions for a GUID +def: "([A-Fa-f0-9]\{8\}-([A-Fa-f0-9]\{4\}-)\{3\}[A-Fa-f0-9]\{12\})." [PSI:PI] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1002232 +name: ProteomeDiscoverer:Default FDR calculator +def: "The default FDR calculator as globally unique identifier (GUID)." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_regexp MS:1002231 ! regular expressions for a GUID + +[Term] +id: MS:1002233 +name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained +def: "Flag indicating if low-resolution spectra are taken into consideration." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002234 +name: selected precursor m/z +def: "Mass-to-charge ratio of a precursor ion selected for fragmentation." [PSI:PI] +synonym: "selected ion m/z" RELATED [] +is_a: MS:1000455 ! ion selection attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002235 +name: ProteoGrouper:PDH score +def: "A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002236 +name: ProteoGrouper:PAG score +def: "A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides." [PSI:PI] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002237 +name: mzidLib +def: "A library of Java routines for manipulating mzIdentML files." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002238 +name: mzidLib:Omssa2Mzid +def: "A converter for OMSSA OMX to mzIdentML." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002239 +name: mzidLib:Tandem2Mzid +def: "A converter for Tandem XML to mzIdentML." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002240 +name: mzidLib:Csv2Mzid +def: "A converter for CSV files (following OMSSA CSV style) to mzIdentML." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002241 +name: mzidLib:ProteoGrouper +def: "A generic and parameterizable protein inference algorithm for mzIdentML files." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002242 +name: mzidLib:Thresholder +def: "A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002243 +name: mzidLib:Perform emPAI on mzid +def: "A routine for adding emPAI quantitative values to an mzIdentML file." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002244 +name: mzidLib:FalseDiscoveryRate +def: "A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002245 +name: mzidLib:Mzidentml2Csv +def: "A tool for converting mzIdentML files to CSV format." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002246 +name: mzidLib:CombineSearchEngines +def: "A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file." [PMID:19253293] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002247 +name: mzidLib:InsertMetaDataFromFasta +def: "A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files." [PSI:PI] +is_a: MS:1002237 ! mzidLib + +[Term] +id: MS:1002248 +name: SEQUEST:spscore +def: "The SEQUEST result 'SpScore'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002249 +name: SEQUEST:sprank +def: "The SEQUEST result 'SpRank'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002250 +name: SEQUEST:deltacnstar +def: "The SEQUEST result 'DeltaCnStar'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002251 +name: Comet +def: "Comet open-source sequence search engine developed at the University of Washington." [PMID:23148064] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002252 +name: Comet:xcorr +def: "The Comet result 'XCorr'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002253 +name: Comet:deltacn +def: "The Comet result 'DeltaCn'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002254 +name: Comet:deltacnstar +def: "The Comet result 'DeltaCnStar'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002255 +name: Comet:spscore +def: "The Comet result 'SpScore'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002256 +name: Comet:sprank +def: "The Comet result 'SpRank'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002257 +name: Comet:expectation value +def: "The Comet result 'Expectation value'." [PSI:PI] +is_a: MS:1001153 ! search engine specific score +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002258 +name: Comet:matched ions +def: "The Comet result 'Matched Ions'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002259 +name: Comet:total ions +def: "The Comet result 'Total Ions'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002260 +name: PSM:FDR threshold +def: "False-discovery rate threshold for peptide-spectrum matches." [PSI:PI] +is_a: MS:1002483 ! PSM-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002261 +name: Byonic +def: "Byonic search engine from Protein Metrics." [PMID:23255153] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002262 +name: Byonic:Score +def: "The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002263 +name: Byonic:Delta Score +def: "The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002264 +name: Byonic:DeltaMod Score +def: "The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002265 +name: Byonic:PEP +def: "Byonic posterior error probability." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002266 +name: Byonic:Peptide LogProb +def: "The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002267 +name: Byonic:Protein LogProb +def: "The log p-value of the protein." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002268 +name: Byonic:Best LogProb +def: "Best (most negative) log p-value of an individual PSM." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002269 +name: Byonic:Best Score +def: "Best (largest) Byonic score of a PSM." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002270 +name: chromatography separation +def: "A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure." [PSI:MS] +is_a: MS:1000857 ! run attribute + +[Term] +id: MS:1002271 +name: liquid chromatography separation +def: "Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid." [PSI:MS] +is_a: MS:1002270 ! chromatography separation + +[Term] +id: MS:1002272 +name: gas chromatography separation +def: "Gas chromatography (GC) is a separation technique in which the mobile phase is a gas." [PSI:MS] +is_a: MS:1002270 ! chromatography separation + +[Term] +id: MS:1002273 +name: detector potential +def: "Detector potential difference in volts." [PSI:MS] +is_a: MS:1000481 ! detector attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002274 +name: SQ Detector 2 +def: "Waters quadrupole based SQ Detector 2." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002275 +name: Xevo G2-S Tof +def: "Waters oa-ToF based Xevo G2-S Tof." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002276 +name: Xevo G2-S QTof +def: "Waters oa-ToF based Xevo G2-S QTof." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002277 +name: AutoSpec Premier +def: "Waters AutoSpec Premier magnetic sector instrument." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002278 +name: Pegasus III +def: "LECO nominal mass resolution time-of-flight GC mass spectrometer." [PSI:MS] +is_a: MS:1001800 ! LECO instrument model + +[Term] +id: MS:1002279 +name: maXis 4G +def: "Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1001547 ! Bruker Daltonics maXis series + +[Term] +id: MS:1002280 +name: compact +def: "Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1002281 +name: SRM feature level quantitation +def: "Selected Reaction Monitoring feature level quantitation." [PSI:PI] +is_a: MS:1001838 ! SRM quantitation analysis + +[Term] +id: MS:1002282 +name: SRM peptide level quantitation +def: "Selected Reaction Monitoring peptide level quantitation." [PSI:PI] +is_a: MS:1001838 ! SRM quantitation analysis + +[Term] +id: MS:1002283 +name: SRM protein level quantitation +def: "Selected Reaction Monitoring protein level quantitation." [PSI:PI] +is_a: MS:1001838 ! SRM quantitation analysis + +[Term] +id: MS:1002284 +name: SRM proteingroup level quantitation +def: "Selected Reaction Monitoring proteingroup level quantitation." [PSI:PI] +is_a: MS:1001838 ! SRM quantitation analysis + +[Term] +id: MS:1002285 +name: Trans-Proteomic Pipeline +def: "A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology." [PSI:PI] +synonym: "TPP" EXACT [] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002286 +name: Trans-Proteomic Pipeline software +def: "A software program that is a component of the Trans-Proteomic Pipeline." [PSI:PI] +is_a: MS:1001456 ! analysis software +relationship: part_of MS:1002285 ! Trans-Proteomic Pipeline + +[Term] +id: MS:1002287 +name: PeptideProphet +def: "A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format." [PMID:12403597, PMID:23176103] +is_a: MS:1002286 ! Trans-Proteomic Pipeline software + +[Term] +id: MS:1002288 +name: iProphet +def: "A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format." [PMID:21876204] +synonym: "InterProphet" EXACT [] +is_a: MS:1002286 ! Trans-Proteomic Pipeline software + +[Term] +id: MS:1002289 +name: ProteinProphet +def: "A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format." [PMID:14632076] +is_a: MS:1002286 ! Trans-Proteomic Pipeline software + +[Term] +id: MS:1002290 +name: XPRESS +def: "A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI] +is_a: MS:1002286 ! Trans-Proteomic Pipeline software + +[Term] +id: MS:1002291 +name: Libra +def: "A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc." [PSI:PI] +is_a: MS:1002286 ! Trans-Proteomic Pipeline software + +[Term] +id: MS:1002292 +name: PTMProphet +def: "A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites." [PSI:PI] +is_a: MS:1002286 ! Trans-Proteomic Pipeline software + +[Term] +id: MS:1002293 +name: Bruker Daltonics SCION series +def: "Bruker Daltonics' SCION series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1002294 +name: Bruker Daltonics EVOQ series +def: "Bruker Daltonics' EVOQ series." [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1002295 +name: SCION SQ +def: "Bruker Daltonics' SCION SQ: GC-single quadrupole." [PSI:MS] +is_a: MS:1002293 ! Bruker Daltonics SCION series + +[Term] +id: MS:1002296 +name: SCION TQ +def: "Bruker Daltonics' SCION TQ: GC-triple quadrupole." [PSI:MS] +is_a: MS:1002293 ! Bruker Daltonics SCION series + +[Term] +id: MS:1002297 +name: EVOQ Elite +def: "Bruker Daltonics' EVOQ Elite: LC-triple quadrupole." [PSI:MS] +is_a: MS:1002294 ! Bruker Daltonics EVOQ series + +[Term] +id: MS:1002298 +name: EVOQ Qube +def: "Bruker Daltonics' EVOQ Qube: LC-triple quadrupole." [PSI:MS] +is_a: MS:1002294 ! Bruker Daltonics EVOQ series + +[Term] +id: MS:1002299 +name: micrOTOF-Q III +def: "Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1002300 +name: amaZon Speed ETD +def: "Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1001545 ! Bruker Daltonics amaZon series + +[Term] +id: MS:1002301 +name: amaZon Speed +def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] +is_a: MS:1001545 ! Bruker Daltonics amaZon series + +[Term] +id: MS:1002302 +name: Bruker Container format +def: "Bruker Container raw file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002303 +name: Bruker Container nativeID format +def: "Native identifier (UUID)." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002304 +name: domain range +def: "Domain range of a numerical value." [PSI:PI] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1002305 +name: value between 0 and 1 inclusive +def: "Value range for probabilities." [PSI:PI] +is_a: MS:1002304 ! domain range + +[Term] +id: MS:1002306 +name: value greater than zero +def: "Positive value range." [PSI:PI] +is_a: MS:1002304 ! domain range + +[Term] +id: MS:1002307 +name: fragmentation ion type +def: "Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion." [PSI:PI] +is_a: MS:1001221 ! product ion attribute + +[Term] +id: MS:1002308 +name: fluorescence detector +def: "A detector using a fluorescent signal after excitation with light." [PSI:MS] +is_a: MS:1000026 ! detector type + +[Term] +id: MS:1002309 +name: Byonic: Peptide AbsLogProb +def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002310 +name: Byonic: Protein AbsLogProb +def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002311 +name: Byonic: Peptide AbsLogProb2D +def: "The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002312 +name: MS-Numpress linear prediction compression +def: "Compression using MS-Numpress linear prediction compression." [https://github.com/ms-numpress/ms-numpress] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1002313 +name: MS-Numpress positive integer compression +def: "Compression using MS-Numpress positive integer compression." [https://github.com/ms-numpress/ms-numpress] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1002314 +name: MS-Numpress short logged float compression +def: "Compression using MS-Numpress short logged float compression." [https://github.com/ms-numpress/ms-numpress] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1002315 +name: consensus result +def: "Indicates a consensus result from several search engine runs." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details + +[Term] +id: MS:1002316 +name: ProteomeDiscoverer:Amanda:high confidence threshold +def: "Strict confidence probability score." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002317 +name: ProteomeDiscoverer:Amanda:middle confidence threshold +def: "Relaxed confidence probability score." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002318 +name: ProteomeDiscoverer:automatic workload +def: "Flag indicating automatic estimation of the workload level." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002319 +name: Amanda:AmandaScore +def: "The Amanda score of the scoring function for a PSM." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002320 +name: ProteomeDiscoverer:max differential modifications +def: "Maximum dynamic modifications per PSM." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002321 +name: ProteomeDiscoverer:max equal modifications +def: "Maximum equal modifications per PSM." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002322 +name: ProteomeDiscoverer:min peptide length +def: "Minimum peptide length." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002323 +name: ProteomeDiscoverer:max peptide length +def: "Maximum peptide length." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002324 +name: ProteomeDiscoverer:max number neutral loss +def: "Maximum number of same neutral losses." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002325 +name: ProteomeDiscoverer:max number neutral loss modifications +def: "Max number of same neutral losses of modifications." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002326 +name: ProteomeDiscoverer:use flanking ions +def: "Flag for usage of flanking ions." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002327 +name: ProteomeDiscoverer:max number of same modifs +def: "The maximum number of possible equal modifications per PSM." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002328 +name: ProteomeDiscoverer:perform deisotoping +def: "Defines whether a simple deisotoping shall be performed." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002329 +name: ProteomeDiscoverer:ion settings +def: "Specifies the fragment ions and neutral losses that are calculated." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002330 +name: ProteomeDiscoverer:3. Static Modification +def: "OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter." [PSI:PI] +comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002331 +name: ProteomeDiscoverer:5. Dynamic Modification +def: "OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter." [PSI:PI] +comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002332 +name: lab head +def: "The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group." [PSI:PI] +is_a: MS:1002033 ! contact role + +[Term] +id: MS:1002333 +name: conversion software +def: "Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process." [PSI:PI] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002334 +name: ProCon +def: "Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML." [PSI:PI, http://www.medizinisches-proteom-center.de/procon] +is_a: MS:1002333 ! conversion software + +[Term] +id: MS:1002335 +name: PRIDE Converter2 +def: "Java software designed to convert one of several proteomics identification results formats into PRIDE XML." [PMID:22949509] +is_a: MS:1002333 ! conversion software + +[Term] +id: MS:1002336 +name: Amanda +def: "Amanda scoring system for PSM identification." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002337 +name: Andromeda +def: "Andromeda is a peptide search engine." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002338 +name: Andromeda:score +def: "The probability based score of the Andromeda search engine." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002339 +name: site:global FDR +def: "Estimation of global false discovery rate of peptides with a post-translational modification." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002340 +name: ProteomeXchange project tag +def: "Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002341 +name: second-pass peptide identification +def: "A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002342 +name: MZmine +def: "A framework for differential analysis of mass spectrometry data." [PMID:16403790, PMID:20650010] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002343 +name: ion stability type +def: "OBSOLETE Stability type of the ion." [PSI:PI] +comment: This child of the former purgatory term ion was made obsolete. +is_obsolete: true + +[Term] +id: MS:1002344 +name: Maltcms +def: "Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers." [PSI:PI, http://maltcms.sf.net] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002345 +name: PSM-level attribute +def: "Attribute of a single peptide-spectrum match." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002346 +name: protein group-level identification attribute +def: "Protein group level information." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002347 +name: PSM-level identification statistic +def: "Identification confidence metric for a peptide spectrum match." [PSI:PI] +is_a: MS:1002345 ! PSM-level attribute + +[Term] +id: MS:1002348 +name: protein group-level identification statistic +def: "Identification confidence metric for a protein group." [PSI:PI] +is_a: MS:1002346 ! protein group-level identification attribute + +[Term] +id: MS:1002349 +name: value greater than zero but less than or equal to one +def: "Positive value range less than or equal to 1." [PSI:PI] +is_a: MS:1002304 ! domain range + +[Term] +id: MS:1002350 +name: PSM-level global FDR +def: "Estimation of the global false discovery rate of peptide spectrum matches." [PSI:PI] +is_a: MS:1002701 ! PSM-level result list statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002351 +name: PSM-level local FDR +def: "Estimation of the local false discovery rate of peptide spectrum matches." [PSI:PI] +is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002352 +name: PSM-level p-value +def: "Estimation of the p-value for peptide spectrum matches." [PSI:PI] +is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002353 +name: PSM-level e-value +def: "Estimation of the e-value for peptide spectrum matches." [PSI:PI] +is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002354 +name: PSM-level q-value +def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI] +is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002355 +name: PSM-level FDRScore +def: "mzidLibrary FDRScore for peptide spectrum matches." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002356 +name: PSM-level combined FDRScore +def: "mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002357 +name: PSM-level probability +def: "Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum." [PSI:PI] +is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002358 +name: search engine specific peptide sequence-level identification statistic +def: "Search engine specific distinct peptide score." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic + +[Term] +id: MS:1002359 +name: peptide sequence-level local FDR +def: "Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002360 +name: distinct peptide-level FDRScore +def: "MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002361 +name: distinct peptide-level combined FDRScore +def: "Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools." [PSI:PI] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002362 +name: peptide sequence-level probability +def: "Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs." [PSI:PI] +is_a: MS:1001092 ! peptide sequence-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002363 +name: search engine specific score for proteins +def: "Search engine specific protein scores." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic + +[Term] +id: MS:1002364 +name: protein-level local FDR +def: "Estimation of the local false discovery rate of proteins." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002365 +name: FDRScore for proteins +def: "MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002366 +name: combined FDRScore for proteins +def: "MzidLibrary Combined FDRScore for proteins." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002367 +name: probability for proteins +def: "Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002368 +name: search engine specific score for protein groups +def: "Search engine specific protein group scores." [PSI:PI] +is_a: MS:1002348 ! protein group-level identification statistic + +[Term] +id: MS:1002369 +name: protein group-level global FDR +def: "Estimation of the global false discovery rate of protein groups." [PSI:PI] +is_a: MS:1002706 ! protein group-level result list statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002370 +name: protein group-level local FDR +def: "Estimation of the local false discovery rate of protein groups." [PSI:PI] +is_a: MS:1002348 ! protein group-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002371 +name: protein group-level p-value +def: "Estimation of the p-value for protein groups." [PSI:PI] +is_a: MS:1002348 ! protein group-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002372 +name: protein group-level e-value +def: "Estimation of the e-value for protein groups." [PSI:PI] +is_a: MS:1002348 ! protein group-level identification statistic +relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002373 +name: protein group-level q-value +def: "Estimation of the q-value for protein groups." [PSI:PI] +is_a: MS:1002348 ! protein group-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002374 +name: protein group-level FDRScore +def: "mzidLibrary FDRScore for protein groups." [PSI:PI] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002375 +name: protein group-level combined FDRScore +def: "mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002376 +name: protein group-level probability +def: "Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] +is_a: MS:1002348 ! protein group-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002377 +name: ProteomeDiscoverer:Relaxed Score Threshold +def: "Specifies the threshold value for relaxed scoring." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002378 +name: ProteomeDiscoverer:Strict Score Threshold +def: "Specifies the threshold value for strict scoring." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002379 +name: ProteomeDiscoverer:Peptide Without Protein Cut Off Score +def: "Cut off score for storing peptides that do not belong to a protein." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002380 +name: false localization rate +def: "Estimation of the false localization rate for modification site assignment." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002381 +name: MALDI Solutions LC-MALDI +def: "Software for automated LC-MALDI analysis and reporting." [PSI:PI] +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software +is_a: MS:1001557 ! Shimadzu Corporation software + +[Term] +id: MS:1002382 +name: Shimadzu MALDI-7090 +def: "Shimadzu MALDI-7090: MALDI-TOF-TOF." [PSI:PI] +is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model + +[Term] +id: MS:1002383 +name: SCiLS software +def: "SCiLS software for data acquisition and analysis." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1002384 +name: SCiLS Lab +def: "SCiLS Lab software." [PSI:MS] +is_a: MS:1002383 ! SCiLS software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002385 +name: SCiLS Lab format +def: "SCiLS Lab file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002386 +name: preprocessing software +def: "Preprocessing software." [PSI:PI] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002387 +name: PIA +def: "PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis." [PSI:PI, http://www.medizinisches-proteom-center.de/pia] +is_a: MS:1002414 ! postprocessing software +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002388 +name: PIA XML format +def: "A compilation of search engine results in the PIA XML format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1002389 +name: PIA workflow parameter +def: "A parameter set for a single PIA analysis." [PSI:PI] +is_a: MS:1002105 ! software specific input parameter +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002390 +name: PIA:FDRScore calculated +def: "Indicates whether the FDR score was calculated for the input file." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002391 +name: PIA:Combined FDRScore calculated +def: "Indicates whether the combined FDR score was calculated for the PIA compilation." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002392 +name: PIA:PSM sets created +def: "Indicates whether PSM sets were created." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002393 +name: PIA:used top identifications for FDR +def: "The number of top identifications per spectrum used for the FDR calculation, 0 means all." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002394 +name: PIA:protein score +def: "The score given to a protein by any protein inference." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002395 +name: PIA:protein inference +def: "The used algorithm for the protein inference using PIA." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002396 +name: PIA:protein inference filter +def: "A filter used by PIA for the protein inference." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002397 +name: PIA:protein inference scoring +def: "The used scoring method for the protein inference using PIA." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002398 +name: PIA:protein inference used score +def: "The used base score for the protein inference using PIA." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002399 +name: PIA:protein inference used PSMs +def: "The method to determine the PSMs used for scoring by the protein inference." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002400 +name: PIA:filter +def: "A filter used for the report generation." [PSI:PI] +is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002401 +name: leading protein +def: "At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members." [PSI:PI] +is_a: MS:1001101 ! protein group or subset relationship + +[Term] +id: MS:1002402 +name: non-leading protein +def: "Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence." [PSI:PI] +is_a: MS:1001101 ! protein group or subset relationship + +[Term] +id: MS:1002403 +name: group representative +def: "An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative." [PSI:PI] +is_a: MS:1001101 ! protein group or subset relationship + +[Term] +id: MS:1002404 +name: count of identified proteins +def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI] +is_a: MS:1002704 ! protein-level result list attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002405 +name: protein group-level result list attribute +def: "Details describing a protein cluster." [PSI:PI] +is_a: MS:1002699 ! result list attribute + +[Term] +id: MS:1002406 +name: count of identified clusters +def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [DOI:10.1002/pmic.201400080, PMID:25092112] +is_a: MS:1002405 ! protein group-level result list attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002407 +name: cluster identifier +def: "An identifier applied to protein groups to indicate that they are linked by shared peptides." [PSI:PI] +is_a: MS:1002698 ! protein cluster identification attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002408 +name: number of distinct protein sequences +def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [PSI:PI] +is_a: MS:1002405 ! protein group-level result list attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002409 +name: marginally distinguished protein +def: "Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group." [PSI:PI] +is_a: MS:1001101 ! protein group or subset relationship + +[Term] +id: MS:1002410 +name: Anubis +def: "Anubis software for selected reaction monitoring data." [PSI:PI, http://quantitativeproteomics.org/anubis] +is_a: MS:1000871 ! SRM software +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1002411 +name: TraML format +def: "The TraML format for transitions in SRM from the PSI. File extension '.TraML'." [PSI:PI, http://www.psidev.info/traml] +is_a: MS:1002128 ! method file format + +[Term] +id: MS:1002412 +name: total XIC area +def: "Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002413 +name: product background +def: "The background area for the quantified transition." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002414 +name: postprocessing software +def: "Postprocessing software." [PSI:PI] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002415 +name: protein group passes threshold +def: "A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file." [PSI:PI] +is_a: MS:1002346 ! protein group-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002416 +name: Orbitrap Fusion +def: "Thermo Scientific Orbitrap Fusion." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002417 +name: Orbitrap Fusion ETD +def: "Thermo Scientific Orbitrap Fusion with ETD." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002418 +name: TSQ Quantiva +def: "Thermo Scientific TSQ Quantiva MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002419 +name: TSQ Endura +def: "Thermo Scientific TSQ Endura MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002420 +name: PASSEL experiment URI +def: "URI that allows access to a PASSEL experiment." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002421 +name: Paragon input parameter +def: "Search engine input parameters specific to Paragon." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002422 +name: Paragon: sample type +def: "The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002423 +name: Paragon: cysteine alkylation +def: "The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002424 +name: Paragon: instrument setting +def: "The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002425 +name: Paragon: search effort +def: "The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002426 +name: Paragon: ID focus +def: "A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002427 +name: Paragon: FDR analysis +def: "The Paragon method setting that controls whether FDR analysis is conducted." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002428 +name: Paragon: quantitation +def: "The Paragon method setting that controls whether quantitation analysis is conducted." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002429 +name: Paragon: background correction +def: "The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002430 +name: Paragon: bias correction +def: "The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002431 +name: Paragon: channel to use as denominator in ratios +def: "The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002432 +name: search engine specific input metadata +def: "Search engine specific metadata that are not user-controlled settings." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1002433 +name: Paragon: modified data dictionary or parameter translation +def: "This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result." [PSI:PI] +is_a: MS:1002432 ! search engine specific input metadata +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002434 +name: number of spectra searched +def: "Number of spectra in a search." [PSI:PI] +is_a: MS:1001249 ! search input details +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002435 +name: data processing start time +def: "The time that a data processing action was started." [PSI:MS] +is_a: MS:1000630 ! data processing parameter +relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term + +[Term] +id: MS:1002436 +name: Paragon: digestion +def: "The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done." [PSI:PI] +is_a: MS:1001249 ! search input details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002437 +name: number of decoy sequences +def: "The number of decoy sequences, if the concatenated target-decoy approach is used." [PSI:PI] +is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002438 +name: spectrum identification list result details +def: "Information about the list of PSMs (SpectrumIdentificationList)." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1002439 +name: final PSM list +def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI] +is_a: MS:1002438 ! spectrum identification list result details + +[Term] +id: MS:1002440 +name: intermediate PSM list +def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI] +is_a: MS:1002438 ! spectrum identification list result details + +[Term] +id: MS:1002441 +name: Andi-MS format +def: "AIA Analytical Data Interchange file format for mass spectrometry data." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002442 +name: chromatograph file format +def: "The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:PI] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1002443 +name: Andi-CHROM format +def: "AIA Analytical Data Interchange file format for chromatography data." [PSI:PI] +is_a: MS:1002442 ! chromatograph file format + +[Term] +id: MS:1002444 +name: 6420 Triple Quadrupole LC/MS +def: "The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002445 +name: 6460 Triple Quadrupole LC/MS +def: "The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002446 +name: 6490 Triple Quadrupole LC/MS +def: "The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002447 +name: Paragon:special factor +def: "The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects." [PSI:PI] +is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002448 +name: PEAKS:inChorusPeptideScore +def: "The PEAKS inChorus peptide score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002449 +name: PEAKS:inChorusProteinScore +def: "The PEAKS inChorus protein score." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002450 +name: param: b ion-H3PO4 DEPRECATED +def: "Ion b-H3PO4: b ion with lost phosphoric acid." [PSI:PI] +is_a: MS:1001066 ! ions series considered in search + +[Term] +id: MS:1002451 +name: param: y ion-H3PO4 DEPRECATED +def: "Ion y-H3PO4: y ion with lost phosphoric acid." [PSI:PI] +is_a: MS:1001066 ! ions series considered in search + +[Term] +id: MS:1002452 +name: Maui +def: "The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002453 +name: No fixed modifications searched +def: "No fixed modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI] +is_a: MS:1002094 ! common search engine input parameter + +[Term] +id: MS:1002454 +name: No variable modifications searched +def: "No variable modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI] +is_a: MS:1002094 ! common search engine input parameter + +[Term] +id: MS:1002455 +name: H2O neutral loss +def: "OBSOLETE Neutral loss of water." [PSI:PI] +comment: This term was obsoleted because it should be replaced by MS:1000336 with value H2O. +is_a: MS:1000336 ! neutral loss +is_a: MS:1002473 ! ion series considered in search +is_obsolete: true + +[Term] +id: MS:1002456 +name: NH3 neutral loss +def: "OBSOLETE Neutral loss of ammonia." [PSI:PI] +comment: This term was obsoleted because it should be replaced by MS:1000336 with value NH3. +is_a: MS:1000336 ! neutral loss +is_a: MS:1002473 ! ion series considered in search +is_obsolete: true + +[Term] +id: MS:1002457 +name: H3PO4 neutral loss +def: "OBSOLETE Neutral loss of phosphoric acid." [PSI:PI] +comment: This term was obsoleted because it should be replaced by MS:1000336 with value H3PO4. +is_a: MS:1000336 ! neutral loss +is_a: MS:1002473 ! ion series considered in search +is_obsolete: true + +[Term] +id: MS:1002458 +name: PeptideShaker +def: "PeptideShaker is a software for the interpretation of proteomics identification results." [PSI:PI, http://peptide-shaker.googlecode.com] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002459 +name: MS Amanda csv format +def: "MS Amanda csv output format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1002460 +name: protein group-level global FNR +def: "Estimation of the global false negative rate of protein groups." [PSI:PI] +is_a: MS:1002706 ! protein group-level result list statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive + +[Term] +id: MS:1002461 +name: protein group-level confidence +def: "Estimation of the global confidence of protein groups." [PSI:PI] +is_a: MS:1002348 ! protein group-level identification statistic + +[Term] +id: MS:1002462 +name: peptide sequence-level global FNR +def: "Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] +is_a: MS:1002703 ! peptide sequence-level result list statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive + +[Term] +id: MS:1002463 +name: peptide sequence-level global confidence +def: "Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] +is_a: MS:1002703 ! peptide sequence-level result list statistic + +[Term] +id: MS:1002464 +name: PSM-level global FNR +def: "Estimation of the global false negative rate of peptide spectrum matches." [PSI:PI] +is_a: MS:1002701 ! PSM-level result list statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive + +[Term] +id: MS:1002465 +name: PSM-level global confidence +def: "Estimation of the global confidence of peptide spectrum matches." [PSI:PI] +is_a: MS:1002701 ! PSM-level result list statistic + +[Term] +id: MS:1002466 +name: PeptideShaker PSM score +def: "The probability based PeptideShaker PSM score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002467 +name: PeptideShaker PSM confidence +def: "The probability based PeptideShaker PSM confidence." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002468 +name: PeptideShaker peptide score +def: "The probability based PeptideShaker peptide score." [PSI:PI] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002469 +name: PeptideShaker peptide confidence +def: "The probability based PeptideShaker peptide confidence." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002470 +name: PeptideShaker protein group score +def: "The probability based PeptideShaker protein group score." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002471 +name: PeptideShaker protein group confidence +def: "The probability based PeptideShaker protein group confidence." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002472 +name: trap-type collision-induced dissociation +def: "A collision-induced dissociation process that occurs in a trap-type collision cell." [PSI:PI] +is_a: MS:1000133 ! collision-induced dissociation + +[Term] +id: MS:1002473 +name: ion series considered in search +def: "The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI] +is_a: MS:1001249 ! search input details + +[Term] +id: MS:1002474 +name: ProteoAnnotator:non-canonical gene model score +def: "The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group." [PSI:PI] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002475 +name: ProteoAnnotator:count alternative peptides +def: "The count of the number of peptide sequences mapped to non-canonical gene models only within the group." [PSI:PI] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002476 +name: ion mobility drift time +def: "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002477 +name: mean ion mobility drift time array +def: "Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002478 +name: mean charge array +def: "Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1002479 +name: regular expression +def: "Regular expression." [PSI:PI] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1002480 +name: regular expression for a digital object identifier (DOI) +def: "(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)." [PSI:PI, http://dx.doi.org/] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1002481 +name: higher energy beam-type collision-induced dissociation +def: "A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS] +is_a: MS:1000422 ! beam-type collision-induced dissociation + +[Term] +id: MS:1002482 +name: statistical threshold +def: "Estimated statistical threshold." [PSI:MS] +is_a: MS:1001060 ! quality estimation method details + +[Term] +id: MS:1002483 +name: PSM-level statistical threshold +def: "Estimated statistical threshold at PSM-level." [PSI:MS] +is_a: MS:1002573 ! spectrum identification statistical threshold + +[Term] +id: MS:1002484 +name: peptide-level statistical threshold +def: "Estimated statistical threshold at peptide-level." [PSI:MS] +is_a: MS:1002573 ! spectrum identification statistical threshold + +[Term] +id: MS:1002485 +name: protein-level statistical threshold +def: "Estimated statistical threshold at protein-level." [PSI:MS] +is_a: MS:1002572 ! protein detection statistical threshold + +[Term] +id: MS:1002486 +name: protein group-level statistical threshold +def: "Estimated statistical threshold at protein group-level." [PSI:PI] +is_a: MS:1002572 ! protein detection statistical threshold + +[Term] +id: MS:1002487 +name: MassIVE dataset identifier +def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002488 +name: MassIVE dataset URI +def: "URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002489 +name: special processing +def: "Details describing a special processing." [PSI:PI] +is_a: MS:1001080 ! search type +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1002490 +name: peptide-level scoring +def: "Peptide-level scoring performed." [PSI:PI] +is_a: MS:1002489 ! special processing + +[Term] +id: MS:1002491 +name: modification localization scoring +def: "Modification localization scoring performed." [PSI:PI] +is_a: MS:1002489 ! special processing + +[Term] +id: MS:1002492 +name: consensus scoring +def: "Consensus multiple search engine approach performed." [PSI:PI] +is_a: MS:1002489 ! special processing + +[Term] +id: MS:1002493 +name: sample pre-fractionation +def: "Sample pre-fractionation performed." [PSI:PI] +is_a: MS:1002489 ! special processing + +[Term] +id: MS:1002494 +name: cross-linking search +def: "Cross-linking search performed." [PSI:PI] +is_a: MS:1002489 ! special processing + +[Term] +id: MS:1002495 +name: no special processing +def: "No special processing performed." [PSI:PI] +is_a: MS:1002489 ! special processing + +[Term] +id: MS:1002496 +name: group PSMs by sequence +def: "Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI] +is_a: MS:1002658 ! identification parameter + +[Term] +id: MS:1002497 +name: group PSMs by sequence with modifications +def: "Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI] +is_a: MS:1002658 ! identification parameter + +[Term] +id: MS:1002498 +name: group PSMs by sequence with modifications and charge +def: "Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI] +is_a: MS:1002658 ! identification parameter + +[Term] +id: MS:1002499 +name: peptide level score +def: "OBSOLETE Peptide level score." [PSI:PI] +comment: This term was obsoleted because it was never intended to go in the CV. +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +is_obsolete: true + +[Term] +id: MS:1002500 +name: peptide passes threshold +def: "A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002501 +name: no PSM threshold +def: "Indicating that no PSM threshold was used." [PSI:PI] +is_a: MS:1002701 ! PSM-level result list statistic + +[Term] +id: MS:1002502 +name: no peptide-level threshold +def: "Indicating that no peptide-level threshold was used." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute + +[Term] +id: MS:1002503 +name: PSM is used for peptide-level scoring +def: "Flags a PSM that it is used for peptide-level scoring." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute + +[Term] +id: MS:1002504 +name: modification index +def: "The order of modifications to be referenced elsewhere in the document." [PSI:PI] +is_a: MS:1001055 ! modification parameters +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002505 +name: regular expression for modification localization scoring +def: "([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})." [PSI:PI] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1002506 +name: modification position score +def: "Modification position score." [PSI:PI] +is_a: MS:1001055 ! modification parameters + +[Term] +id: MS:1002507 +name: modification rescoring:false localization rate +def: "Mod position score: false localization rate." [PSI:PI] +is_a: MS:1002506 ! modification position score +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002508 +name: cross-linking attribute +def: "Cross-linking attribute." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002509 +name: cross-link donor +def: "The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] +is_a: MS:1002508 ! cross-linking attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002510 +name: cross-link acceptor +def: "Cross-linking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] +is_a: MS:1002508 ! cross-linking attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002511 +name: cross-link spectrum identification item +def: "Cross-linked spectrum identification item." [PSI:PI] +is_a: MS:1002508 ! cross-linking attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002512 +name: cross-linking score +def: "Cross-linking scoring value." [PSI:PI] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002513 +name: molecules per cell +def: "The absolute abundance of protein in a cell." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002514 +name: absolute quantitation analysis +def: "Absolute quantitation analysis." [PSI:PI] +is_a: MS:1001833 ! quantitation analysis summary + +[Term] +id: MS:1002515 +name: internal peptide reference used +def: "States whether an internal peptide reference is used or not in absolute quantitation analysis." [PSI:PI] +is_a: MS:1001832 ! quantitation software comment or customizations +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002516 +name: internal protein reference used +def: "States whether an internal protein reference is used or not in absolute quantitation analysis." [PSI:PI] +is_a: MS:1001832 ! quantitation software comment or customizations +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002517 +name: internal reference abundance +def: "The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis." [PSI:PI] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002518 +name: Progenesis:protein group normalised abundance +def: "The data type normalised abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] +is_a: MS:1002739 ! protein group-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002519 +name: Progenesis:protein group raw abundance +def: "The data type raw abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] +is_a: MS:1002739 ! protein group-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002520 +name: peptide group ID +def: "Peptide group identifier for peptide-level stats." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002521 +name: mass spectrometry imaging +def: "A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position." [PSI:PI] +is_a: MS:1000857 ! run attribute + +[Term] +id: MS:1002522 +name: ProteomeDiscoverer:1. Static Terminal Modification +def: "Determine 1st static terminal post-translational modifications (PTMs)." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002523 +name: Q Exactive HF +def: "Thermo Scientific Q Exactive." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002524 +name: PepFinder +def: "Thermo Scientific PepFinder BioPharma analysis software." [PSI:PI] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002525 +name: TSQ 8000 Evo +def: "Thermo Scientific TSQ 8000 Evo MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002526 +name: Exactive Plus +def: "Thermo Scientific Exactive Plus MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002527 +name: instrument specific scan attribute +def: "Instrument specific scan properties that are associated with a value." [PSI:PI] +is_a: MS:1000503 ! scan attribute + +[Term] +id: MS:1002528 +name: synchronous prefilter selection +def: "Synchronous prefilter selection." [PSI:PI] +synonym: "SPS" EXACT [] +is_a: MS:1002527 ! instrument specific scan attribute + +[Term] +id: MS:1002529 +name: resolution array +def: "A data array of resolution values." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1002530 +name: baseline array +def: "A data array of signal baseline values (the signal in the absence of analytes)." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1002531 +name: UIMF format +def: "SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002532 +name: UIMF nativeID format +def: "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1002533 +name: TripleTOF 6600 +def: "SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002534 +name: ProLuCID:xcorr +def: "The ProLuCID result 'XCorr'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002535 +name: ProLuCID:deltacn +def: "The ProLuCID result 'DeltaCn'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002536 +name: D-Score +def: "D-Score for PTM site location at the PSM-level." [PMID:23307401] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002537 +name: MD-Score +def: "MD-Score for PTM site location at the PSM-level." [PMID:21057138] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002538 +name: PTM localization confidence metric +def: "Localization confidence metric for a post translational modification (PTM)." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002539 +name: PeptideShaker PTM confidence type +def: "PeptideShaker quality criteria for the confidence of PTM localizations." [PSI:PI] +is_a: MS:1002538 ! PTM localization confidence metric +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002540 +name: PeptideShaker PSM confidence type +def: "PeptideShaker quality criteria for the confidence of PSM's." [PSI:PI] +is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002541 +name: PeptideShaker peptide confidence type +def: "PeptideShaker quality criteria for the confidence of peptide identifications." [PSI:PI] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002542 +name: PeptideShaker protein confidence type +def: "PeptideShaker quality criteria for the confidence of protein identifications." [PSI:PI] +is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002543 +name: xiFDR +def: "Target/Decoy based FDR estimation for cross-linking peptide-identifications." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002544 +name: xi +def: "Search engine for cross-linked peptides." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002545 +name: xi:score +def: "The xi result 'Score'." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002546 +name: Skyline mzQuantML converter +def: "A software package to convert Skyline report to mzQuantML." [PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002547 +name: normalized spectral abundance factor +def: "A normalized spectral abundance factor (NSAF)." [DOI:10.1021/pr060161n, PMID:16944946] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002548 +name: distributed normalized spectral abundance factor +def: "A distributed normalized spectral abundance factor (dNSAF)." [DOI:10.1021/ac9023999, PMID:20166708] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002549 +name: PTM localization distinct peptide-level statistic +def: "Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence." [PSI:PI] +is_a: MS:1002689 ! PTM localization single result statistic + +[Term] +id: MS:1002550 +name: peptide:phosphoRS score +def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI] +is_a: MS:1002549 ! PTM localization distinct peptide-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002551 +name: peptide:Ascore +def: "A-score for PTM site location at the peptide-level." [PSI:PI] +is_a: MS:1002549 ! PTM localization distinct peptide-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002552 +name: peptide:H-Score +def: "H-Score for peptide phosphorylation site location at the peptide-level." [PSI:PI] +is_a: MS:1002549 ! PTM localization distinct peptide-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002553 +name: peptide:D-Score +def: "D-Score for PTM site location at the peptide-level." [PSI:PI] +is_a: MS:1002549 ! PTM localization distinct peptide-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002554 +name: peptide:MD-Score +def: "MD-Score for PTM site location at the peptide-level." [PSI:PI] +is_a: MS:1002549 ! PTM localization distinct peptide-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002555 +name: PTM localization score threshold +def: "Threshold for PTM site location score." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details + +[Term] +id: MS:1002556 +name: Ascore threshold +def: "Threshold for Ascore PTM site location score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002557 +name: D-Score threshold +def: "Threshold for D-score PTM site location score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002558 +name: MD-Score threshold +def: "Threshold for MD-score PTM site location score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002559 +name: H-Score threshold +def: "Threshold for H-score PTM site location score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002560 +name: DeBunker:score threshold +def: "Threshold for DeBunker PTM site location score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002561 +name: Mascot:PTM site assignment confidence threshold +def: "Threshold for Mascot PTM site assignment confidence." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002562 +name: MSQuant:PTM-score threshold +def: "Threshold for MSQuant:PTM-score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002563 +name: MaxQuant:PTM Score threshold +def: "Threshold for MaxQuant:PTM Score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002564 +name: MaxQuant:P-site localization probability threshold +def: "Threshold for MaxQuant:P-site localization probability." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002565 +name: MaxQuant:PTM Delta Score threshold +def: "Threshold for MaxQuant:PTM Delta Score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002566 +name: MaxQuant:Phospho (STY) Probabilities threshold +def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002567 +name: phosphoRS score threshold +def: "Threshold for phosphoRS score." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002568 +name: phosphoRS site probability threshold +def: "Threshold for phosphoRS site probability." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002569 +name: ProteomeDiscoverer:Number of Spectra Processed At Once +def: "Number of spectra processed at once in a ProteomeDiscoverer search." [PSI:PI] +is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002570 +name: sequence multiply subsumable protein +def: "A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002571 +name: spectrum multiply subsumable protein +def: "A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] +is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002572 +name: protein detection statistical threshold +def: "Estimated statistical threshold used for protein detection." [PSI:MS] +is_a: MS:1002482 ! statistical threshold + +[Term] +id: MS:1002573 +name: spectrum identification statistical threshold +def: "Estimated statistical threshold used for spectrum identification." [PSI:MS] +is_a: MS:1002482 ! statistical threshold + +[Term] +id: MS:1002574 +name: ASAPRatio +def: "A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI] +is_a: MS:1002286 ! Trans-Proteomic Pipeline software + +[Term] +id: MS:1002575 +name: Tide +def: "Tide open-source sequence search program developed at the University of Washington." [PMID:21761931] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002576 +name: Andromeda result format +def: "Andromeda result file output format." [PSI:PI] +is_a: MS:1001040 ! intermediate analysis format + +[Term] +id: MS:1002577 +name: 2000 QTRAP +def: "SCIEX 2000 QTRAP." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002578 +name: 2500 QTRAP +def: "SCIEX 2500 QTRAP." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002579 +name: 3500 QTRAP +def: "SCIEX 3500 QTRAP." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002580 +name: QTRAP 4500 +def: "SCIEX QTRAP 4500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002581 +name: QTRAP 6500 +def: "SCIEX QTRAP 6500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002582 +name: QTRAP 6500+ +def: "SCIEX QTRAP 6500+." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002583 +name: TripleTOF 4600 +def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002584 +name: TripleTOF 5600+ +def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002585 +name: API 100 +def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002586 +name: API 100LC +def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002587 +name: API 165 +def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002588 +name: API 300 +def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002589 +name: API 350 +def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002590 +name: API 365 +def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002591 +name: Triple Quad 3500 +def: "SCIEX Triple Quad 3500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002592 +name: Triple Quad 4500 +def: "SCIEX Triple Quad 4500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002593 +name: Triple Quad 5500 +def: "SCIEX Triple Quad 5500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002594 +name: Triple Quad 6500 +def: "SCIEX Triple Quad 6500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002595 +name: Triple Quad 6500+ +def: "SCIEX Triple Quad 6500+." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002596 +name: ProLuCID +def: "The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute." [PMID:26171723] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002597 +name: MS1 format +def: "MS1 file format for MS1 spectral data." [PMID:15317041, DOI:10.1002/rcm.1603] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002598 +name: DTASelect +def: "Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches." [PMID:12643522, http://fields.scripps.edu/DTASelect/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002599 +name: splash key +def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832] +is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002600 +name: PRIDE XML +def: "Internal data and submission format of the PRIDE database." [http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd] +is_a: MS:1002130 ! identification file format +is_a: MS:1001405 ! spectrum identification result details + +[Term] +id: MS:1002601 +name: mzTab +def: "Tabular result format for proteomics and metabolomics experiments." [PMID:24980485, http://www.psidev.info/mztab/] +is_a: MS:1000914 ! tab delimited text format + +[Term] +id: MS:1002602 +name: sample label +def: "Reagent used in labeled quantification methods." [PSI:PI] +is_a: MS:1002111 ! assay label attribute +is_a: MS:1000548 ! sample attribute + +[Term] +id: MS:1002603 +name: ICAT reagent +def: "Isotope coded affinity tag reagent." [PSI:PI] +is_a: MS:1002602 ! sample label + +[Term] +id: MS:1002604 +name: ICAT heavy reagent +def: "The name of the sample labelled with the heavy ICAT label." [PSI:PI] +is_a: MS:1002603 ! ICAT reagent + +[Term] +id: MS:1002605 +name: ICAT light reagent +def: "The name of the sample labelled with the light ICAT label." [PSI:PI] +is_a: MS:1002603 ! ICAT reagent + +[Term] +id: MS:1002606 +name: ICPL reagent +def: "Isotope coded protein labeling reagent." [PSI:PI] +is_a: MS:1002602 ! sample label + +[Term] +id: MS:1002607 +name: ICPL reagent 0 +def: "The name of the sample labelled with the ICPL reagent 0." [PSI:PI] +is_a: MS:1002606 ! ICPL reagent + +[Term] +id: MS:1002608 +name: ICPL reagent 4 +def: "The name of the sample labelled with the ICPL reagent 4." [PSI:PI] +is_a: MS:1002606 ! ICPL reagent + +[Term] +id: MS:1002609 +name: ICPL reagent 6 +def: "The name of the sample labelled with the ICPL reagent 6." [PSI:PI] +is_a: MS:1002606 ! ICPL reagent + +[Term] +id: MS:1002610 +name: ICPL reagent 10 +def: "The name of the sample labelled with the ICPL reagent 10." [PSI:PI] +is_a: MS:1002606 ! ICPL reagent + +[Term] +id: MS:1002611 +name: SILAC reagent +def: "Stable isotope labeling with amino acids in cell culture reagent." [PSI:PI] +is_a: MS:1002602 ! sample label + +[Term] +id: MS:1002612 +name: SILAC heavy reagent +def: "The name of the sample labelled with the heavy SILAC label." [PSI:PI] +is_a: MS:1002611 ! SILAC reagent + +[Term] +id: MS:1002613 +name: SILAC medium reagent +def: "The name of the sample labelled with the medium SILAC label." [PSI:PI] +is_a: MS:1002611 ! SILAC reagent + +[Term] +id: MS:1002614 +name: SILAC light reagent +def: "The name of the sample labelled with the light SILAC label." [PSI:PI] +is_a: MS:1002611 ! SILAC reagent + +[Term] +id: MS:1002615 +name: TMT reagent +def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling." [PSI:PI] +is_a: MS:1002602 ! sample label + +[Term] +id: MS:1002616 +name: TMT reagent 126 +def: "The name of the sample labelled with the TMT reagent 126." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002617 +name: TMT reagent 127 +def: "The name of the sample labelled with the TMT reagent 127." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002618 +name: TMT reagent 128 +def: "The name of the sample labelled with the TMT reagent 128." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002619 +name: TMT reagent 129 +def: "The name of the sample labelled with the TMT reagent 129." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002620 +name: TMT reagent 130 +def: "The name of the sample labelled with the TMT reagent 130." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002621 +name: TMT reagent 131 +def: "The name of the sample labelled with the TMT reagent 131." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002622 +name: iTRAQ reagent +def: "Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent." [PSI:PI] +is_a: MS:1002602 ! sample label + +[Term] +id: MS:1002623 +name: iTRAQ reagent 113 +def: "The name of the sample labelled with the iTRAQ reagent 113." [PSI:PI] +is_a: MS:1002622 ! iTRAQ reagent + +[Term] +id: MS:1002624 +name: iTRAQ reagent 114 +def: "The name of the sample labelled with the iTRAQ reagent 114." [PSI:PI] +is_a: MS:1002622 ! iTRAQ reagent + +[Term] +id: MS:1002625 +name: iTRAQ reagent 115 +def: "The name of the sample labelled with the iTRAQ reagent 115." [PSI:PI] +is_a: MS:1002622 ! iTRAQ reagent + +[Term] +id: MS:1002626 +name: iTRAQ reagent 116 +def: "The name of the sample labelled with the iTRAQ reagent 116." [PSI:PI] +is_a: MS:1002622 ! iTRAQ reagent + +[Term] +id: MS:1002627 +name: iTRAQ reagent 117 +def: "The name of the sample labelled with the iTRAQ reagent 117." [PSI:PI] +is_a: MS:1002622 ! iTRAQ reagent + +[Term] +id: MS:1002628 +name: iTRAQ reagent 118 +def: "The name of the sample labelled with the iTRAQ reagent 118." [PSI:PI] +is_a: MS:1002622 ! iTRAQ reagent + +[Term] +id: MS:1002629 +name: iTRAQ reagent 119 +def: "The name of the sample labelled with the iTRAQ reagent 119." [PSI:PI] +is_a: MS:1002622 ! iTRAQ reagent + +[Term] +id: MS:1002630 +name: iTRAQ reagent 121 +def: "The name of the sample labelled with the iTRAQ reagent 121." [PSI:PI] +is_a: MS:1002622 ! iTRAQ reagent + +[Term] +id: MS:1002631 +name: electron-transfer/higher-energy collision dissociation +def: "Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI] +synonym: "EThcD" EXACT [] +is_a: MS:1003181 ! combined dissociation method + +[Term] +id: MS:1002632 +name: jPOST dataset identifier +def: "Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002633 +name: jPOST dataset URI +def: "URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002634 +name: Q Exactive Plus +def: "Thermo Scientific Q Exactive Plus." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002635 +name: proteogenomics search +def: "Proteogenomics search performed." [PSI:PI] +is_a: MS:1002489 ! special processing + +[Term] +id: MS:1002636 +name: proteogenomics attribute +def: "Proteogenomics attribute." [PSI:PI] +is_a: MS:1001105 ! peptide sequence-level identification attribute + +[Term] +id: MS:1002637 +name: chromosome name +def: "The name or number of the chromosome to which a given peptide has been mapped." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002638 +name: chromosome strand +def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002639 +name: peptide start on chromosome +def: "OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system." [PSI:PI] +comment: This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome. +is_a: MS:1002636 ! proteogenomics attribute +is_obsolete: true +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002640 +name: peptide end on chromosome +def: "The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002641 +name: peptide exon count +def: "The number of exons to which the peptide has been mapped." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002642 +name: peptide exon nucleotide sizes +def: "A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002643 +name: peptide start positions on chromosome +def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002644 +name: genome reference version +def: "The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002645 +name: MSDK +def: "Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data." [PSI:PI, http://msdk.github.io/] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002646 +name: native spectrum identifier format, combined spectra +def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI] +synonym: "nativeID format, combined spectra" EXACT [] +relationship: part_of MS:1000577 ! source data file + +[Term] +id: MS:1002647 +name: Thermo nativeID format, combined spectra +def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002648 +name: Waters nativeID format, combined spectra +def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002649 +name: WIFF nativeID format, combined spectra +def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002650 +name: Bruker/Agilent YEP nativeID format, combined spectra +def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002651 +name: Bruker BAF nativeID format, combined spectra +def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002652 +name: Bruker FID nativeID format, combined spectra +def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +comment: The nativeID must be the same as the source file ID. +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002653 +name: multiple peak list nativeID format, combined spectra +def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002654 +name: single peak list nativeID format, combined spectra +def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002655 +name: scan number only nativeID format, combined spectra +def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002656 +name: spectrum identifier nativeID format, combined spectra +def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +comment: Used for conversion from mzData. The spectrum id attribute is referenced. +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002657 +name: mzML unique identifier, combined spectra +def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +comment: A unique identifier of a spectrum stored in an mzML file. +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002658 +name: identification parameter +def: "Identification parameter for the search engine run." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1002659 +name: UniProtKB text sequence format +def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1002660 +name: UniProtKB XML sequence format +def: "XML-based format used by UniProtKB for sequence entries." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1002661 +name: Morpheus +def: "Morpheus search engine." [PMID:23323968] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002662 +name: Morpheus:Morpheus score +def: "Morpheus score for PSMs." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002663 +name: Morpheus:summed Morpheus score +def: "Summed Morpheus score for protein groups." [PSI:PI] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002664 +name: interaction score derived from cross-linking +def: "Parent term for interaction scores derived from cross-linking." [PSI:PI] +is_a: MS:1002675 ! cross-linking result details +relationship: has_regexp MS:1002665 ! ([0-9]+)[.]([a|b]):([0-9]+|null):([\-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][+-][0-9]+)?):(true|false) +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002665 +name: regular expression for interaction scores derived from cross-linking +def: "([0-9]+)[.]([a|b]):([0-9]+|null):([\-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][+-][0-9]+)?):(true|false)" [PSI:PI] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1002666 +name: impact II +def: "Bruker Daltonics' impact II." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1002667 +name: impact HD +def: "Bruker Daltonics' impact HD." [PSI:MS] +is_a: MS:1001536 ! Bruker Daltonics micrOTOF series + +[Term] +id: MS:1002668 +name: frag: iTRAQ 4plex reporter ion +def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002669 +name: frag: iTRAQ 8plex reporter ion +def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002670 +name: frag: TMT reporter ion +def: "Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002671 +name: frag: TMT ETD reporter ion +def: "Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002672 +name: no modification threshold +def: "No statistical threshold for accepting or rejecting that a modification position." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold + +[Term] +id: MS:1002673 +name: OpenXQuest +def: "Cross-Linking MS search engine." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1002674 +name: X500R QTOF +def: "SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1002675 +name: cross-linking result details +def: "This subsection describes terms which can describe details of cross-linking results." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1002676 +name: protein-pair-level global FDR +def: "Estimation of the global false discovery rate of proteins-pairs in cross-linking experiments." [PSI:PI] +is_a: MS:1002664 ! interaction score derived from cross-linking +relationship: has_domain MS:1003277 ! value between -1 and 1 inclusive +relationship: has_regexp MS:1002665 ! ([0-9]+)[.]([a|b]):([0-9]+|null):([\-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][+-][0-9]+)?):(true|false) +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002677 +name: residue-pair-level global FDR +def: "Estimation of the global false discovery rate of residue-pairs in cross-linking experiments." [PSI:PI] +is_a: MS:1002664 ! interaction score derived from cross-linking +relationship: has_domain MS:1003277 ! value between -1 and 1 inclusive +relationship: has_regexp MS:1002665 ! ([0-9]+)[.]([a|b]):([0-9]+|null):([\-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][+-][0-9]+)?):(true|false) +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002678 +name: supplemental beam-type collision-induced dissociation +def: "A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation." [PSI:MS] +is_a: MS:1000422 ! beam-type collision-induced dissociation + +[Term] +id: MS:1002679 +name: supplemental collision-induced dissociation +def: "The dissociation of an ion after supplemental collisional excitation." [PSI:MS] +is_a: MS:1000133 ! collision-induced dissociation + +[Term] +id: MS:1002680 +name: supplemental collision energy +def: "Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002681 +name: OpenXQuest:combined score +def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002682 +name: OpenXQuest:xcorr xlink +def: "OpenXQuest's cross-correlation of cross-linked ions subscore." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002683 +name: OpenXQuest:xcorr common +def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002684 +name: OpenXQuest:match-odds +def: "OpenXQuest's match-odds subscore." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002685 +name: OpenXQuest:intsum +def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002686 +name: OpenXQuest:wTIC +def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002687 +name: analysis attribute +def: "Attribute of an item in the result of mass spectrometry proteomics data analysis." [PSI:PI] +is_a: MS:1001405 ! spectrum identification result details + +[Term] +id: MS:1002688 +name: PTM localization attribute +def: "Statistic derived from a post-translational modification localization analysis." [PSI:PI] +is_a: MS:1002687 ! analysis attribute + +[Term] +id: MS:1002689 +name: PTM localization single result statistic +def: "Statistic for a single item derived from a post-translational modification localization analysis." [PSI:PI] +is_a: MS:1002688 ! PTM localization attribute + +[Term] +id: MS:1002690 +name: PTM localization result list statistic +def: "Statistic for all items derived from a post-translational modification localization analysis." [PSI:PI] +is_a: MS:1002688 ! PTM localization attribute + +[Term] +id: MS:1002691 +name: global FLR +def: "Global false localization rate for all localizations in a dataset." [PSI:PI] +is_a: MS:1002690 ! PTM localization result list statistic + +[Term] +id: MS:1002692 +name: local FLR at threshold +def: "Local false localization rate for the bottom item in list of localizations sorted from most to least confident." [PSI:PI] +is_a: MS:1002690 ! PTM localization result list statistic + +[Term] +id: MS:1002693 +name: identification attribute +def: "Attribute of an identification item in the result of mass spectrometry proteomics data analysis." [PSI:PI] +is_a: MS:1002687 ! analysis attribute + +[Term] +id: MS:1002694 +name: single identification result attribute +def: "Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis." [PSI:PI] +is_a: MS:1002693 ! identification attribute + +[Term] +id: MS:1002695 +name: frag: isobaric label ion +def: "Fragment ion corresponding to an isobaric label artifact." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1002697 +name: secondary isotope peak +def: "Fragment ion is an isotopic peak other than that monoisotopic peak. This is used in conjuction with another ion type, such as frag: y ion." [PSI:PI] +is_a: MS:1002307 ! fragmentation ion type + +[Term] +id: MS:1002698 +name: protein cluster identification attribute +def: "An attribute of the protein cluster concept as used in mzIdentML." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002699 +name: result list attribute +def: "General property of an entire result list." [PSI:PI] +is_a: MS:1002693 ! identification attribute + +[Term] +id: MS:1002700 +name: PSM-level result list attribute +def: "General property of the list of all PSMs." [PSI:PI] +is_a: MS:1002699 ! result list attribute + +[Term] +id: MS:1002701 +name: PSM-level result list statistic +def: "Statistic pertaining to the full list of all PSMs." [PSI:PI] +is_a: MS:1002700 ! PSM-level result list attribute + +[Term] +id: MS:1002702 +name: peptide sequence-level result list attribute +def: "General property of all peptide sequences in the list." [PSI:PI] +is_a: MS:1002699 ! result list attribute + +[Term] +id: MS:1002703 +name: peptide sequence-level result list statistic +def: "Statistic pertaining to all peptide sequences in the list." [PSI:PI] +is_a: MS:1002702 ! peptide sequence-level result list attribute + +[Term] +id: MS:1002704 +name: protein-level result list attribute +def: "Attribute of an entire protein list." [PSI:PI] +is_a: MS:1002699 ! result list attribute + +[Term] +id: MS:1002705 +name: protein-level result list statistic +def: "A statistical metric of an entire protein list." [PSI:PI] +is_a: MS:1002704 ! protein-level result list attribute + +[Term] +id: MS:1002706 +name: protein group-level result list statistic +def: "Attrbiute of an entire list of protein groups." [PSI:PI] +is_a: MS:1002405 ! protein group-level result list attribute + +[Term] +id: MS:1002707 +name: (?=[KR]) +def: "Regular expression for LysargiNase." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1002708 +name: LysargiNase +def: "Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues." [PMID:25419962] +synonym: "Tryp-N" EXACT [] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1002707 ! (?=[KR]) + +[Term] +id: MS:1002709 +name: compound data type +def: "A data type representing more than a single value." [] + +[Term] +id: MS:1002710 +name: list of type +def: "A data type defining a list of values of a single type." [] +is_a: MS:1002709 ! compound data type + +[Term] +id: MS:1002711 +name: list of strings +def: "A list of xsd:string." [] +is_a: MS:1002710 ! list of type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002712 +name: list of integers +def: "A list of xsd:integer." [] +is_a: MS:1002710 ! list of type +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002713 +name: list of floats +def: "A list of xsd:float." [] +is_a: MS:1002710 ! list of type +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002719 +name: Pegasus BT +def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1001800 ! LECO instrument model + +[Term] +id: MS:1002720 +name: MSPathFinder +def: "PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002721 +name: MSPathFinder:SpecEValue +def: "MSPathFinder spectral E-value." [PSI:PI] +is_a: MS:1002353 ! PSM-level e-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002722 +name: MSPathFinder:EValue +def: "MSPathFinder E-value." [PSI:PI] +is_a: MS:1002353 ! PSM-level e-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002723 +name: MSPathFinder:QValue +def: "MSPathFinder Q-value." [PSI:PI] +is_a: MS:1002354 ! PSM-level q-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002724 +name: MSPathFinder:PepQValue +def: "MSPathFinder peptide-level Q-value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002725 +name: MSPathFinder:RawScore +def: "MSPathFinder raw score." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002726 +name: SYNAPT G2-Si +def: "Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002727 +name: MALDI SYNAPT G2-Si +def: "Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002728 +name: Vion IMS QTof +def: "Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002729 +name: Xevo G2-XS Tof +def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002730 +name: Xevo TQ-XS +def: "Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002731 +name: Xevo TQ-S micro +def: "Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1002732 +name: Orbitrap Fusion Lumos +def: "Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002733 +name: peptide-level spectral count +def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002734 +name: peptide ion-level spectral count +def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] +is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1002735 +name: feature-level quantification datatype +def: "The data type of the value reported in a QuantLayer for a feature." [PSI:PI] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002736 +name: PSM-level quantification datatype +def: "The data type of the value reported in a QuantLayer for a PSM." [PSI:PI] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002737 +name: peptide-level quantification datatype +def: "The data type of the value reported in a QuantLayer for a peptide." [PSI:PI] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002738 +name: protein-level quantification datatype +def: "The data type of the value reported in a QuantLayer for a protein." [PSI:PI] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002739 +name: protein group-level quantification datatype +def: "The data type of the value reported in a QuantLayer for a protein group." [PSI:PI] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002740 +name: unmapped peptide +def: "Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute + +[Term] +id: MS:1002741 +name: unmapped protein +def: "Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location." [PSI:PI] +is_a: MS:1002636 ! proteogenomics attribute + +[Term] +id: MS:1002742 +name: noise array +def: "A data array of noise values." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1002743 +name: sampled noise m/z array +def: "A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array)." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units MS:1000040 ! m/z + +[Term] +id: MS:1002744 +name: sampled noise intensity array +def: "A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array)." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units MS:1000131 ! number of detector counts + +[Term] +id: MS:1002745 +name: sampled noise baseline array +def: "A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array)." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1002746 +name: MS-Numpress linear prediction compression followed by zlib compression +def: "Compression using MS-Numpress linear prediction compression and zlib." [https://github.com/ms-numpress/ms-numpress] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1002747 +name: MS-Numpress positive integer compression followed by zlib compression +def: "Compression using MS-Numpress positive integer compression and zlib." [https://github.com/ms-numpress/ms-numpress] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1002748 +name: MS-Numpress short logged float compression followed by zlib compression +def: "Compression using MS-Numpress short logged float compression and zlib." [https://github.com/ms-numpress/ms-numpress] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1002749 +name: Mascot:IntegratedSpectralLibrarySearch +def: "Means that Mascot has integrated the search results of database and spectral library search into a single data set." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002750 +name: NIST MSPepSearch +def: "Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002751 +name: NIST MSP format +def: "MSP text format defined by the NIST." [PSI:PI] +is_a: MS:1001347 ! database file formats + +[Term] +id: MS:1002752 +name: database type spectral library +def: "Database containing spectra." [PSI:PI] +is_a: MS:1001073 ! database type amino acid + +[Term] +id: MS:1002753 +name: value between 0 and 1000 inclusive +def: "Value range for scores." [PSI:PI] +is_a: MS:1002304 ! domain range + +[Term] +id: MS:1002754 +name: MSPepSearch:score +def: "MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_domain MS:1002753 ! value between 0 and 1000 inclusive + +[Term] +id: MS:1002755 +name: combined ms-ms + spectral library search +def: "A combined MS2 (with fragment ions) and spectral library search." [PSI:PI] +is_a: MS:1001080 ! search type + +[Term] +id: MS:1002756 +name: iodoTMT quantitation analysis +def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002757 +name: glyco-TMT quantitation analysis +def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, PMID:22455665] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002758 +name: aminoxyTMT quantitation analysis +def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, PMID:25337643] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002759 +name: hydrazideTMT quantitation analysis +def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, PMID:25337643] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002760 +name: iTRAQH quantitation analysis +def: "Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow." [PSI:PI, PMID:22926130] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002761 +name: DiART quantitation analysis +def: "Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, PMID:20715779] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002762 +name: DiLeu quantitation analysis +def: "Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779] +is_a: MS:1002009 ! isobaric label quantitation analysis + +[Term] +id: MS:1002763 +name: TMT reagent 127N +def: "The name of the sample labelled with the TMT reagent 127N." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002764 +name: TMT reagent 127C +def: "The name of the sample labelled with the TMT reagent 127C." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002765 +name: TMT reagent 128N +def: "The name of the sample labelled with the TMT reagent 128N." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002766 +name: TMT reagent 128C +def: "The name of the sample labelled with the TMT reagent 128C." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002767 +name: TMT reagent 129N +def: "The name of the sample labelled with the TMT reagent 129N." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002768 +name: TMT reagent 129C +def: "The name of the sample labelled with the TMT reagent 129C." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002769 +name: TMT reagent 130N +def: "The name of the sample labelled with the TMT reagent 130N." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002770 +name: TMT reagent 130C +def: "The name of the sample labelled with the TMT reagent 130C." [PSI:PI] +is_a: MS:1002615 ! TMT reagent + +[Term] +id: MS:1002771 +name: DiART reagent +def: "Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI] +is_a: MS:1002602 ! sample label + +[Term] +id: MS:1002772 +name: DiART reagent 114 +def: "The name of the sample labelled with the DiART reagent 114." [PSI:PI] +is_a: MS:1002771 ! DiART reagent + +[Term] +id: MS:1002773 +name: DiART reagent 115 +def: "The name of the sample labelled with the DiART reagent 115." [PSI:PI] +is_a: MS:1002771 ! DiART reagent + +[Term] +id: MS:1002774 +name: DiART reagent 116 +def: "The name of the sample labelled with the DiART reagent 116." [PSI:PI] +is_a: MS:1002771 ! DiART reagent + +[Term] +id: MS:1002775 +name: DiART reagent 117 +def: "The name of the sample labelled with the DiART reagent 117." [PSI:PI] +is_a: MS:1002771 ! DiART reagent + +[Term] +id: MS:1002776 +name: DiART reagent 118 +def: "The name of the sample labelled with the DiART reagent 118." [PSI:PI] +is_a: MS:1002771 ! DiART reagent + +[Term] +id: MS:1002777 +name: DiART reagent 119 +def: "The name of the sample labelled with the DiART reagent 119." [PSI:PI] +is_a: MS:1002771 ! DiART reagent + +[Term] +id: MS:1002778 +name: DiLeu reagent +def: "Dimethyl leucine labeling reagent." [PSI:PI] +is_a: MS:1002602 ! sample label + +[Term] +id: MS:1002779 +name: DiLeu reagent 115 +def: "The name of the sample labelled with the DiLeu reagent 115." [PSI:PI] +is_a: MS:1002778 ! DiLeu reagent + +[Term] +id: MS:1002780 +name: DiLeu reagent 116 +def: "The name of the sample labelled with the DiLeu reagent 116." [PSI:PI] +is_a: MS:1002778 ! DiLeu reagent + +[Term] +id: MS:1002781 +name: DiLeu reagent 117 +def: "The name of the sample labelled with the DiLeu reagent 117." [PSI:PI] +is_a: MS:1002778 ! DiLeu reagent + +[Term] +id: MS:1002782 +name: DiLeu reagent 118 +def: "The name of the sample labelled with the DiLeu reagent 118." [PSI:PI] +is_a: MS:1002778 ! DiLeu reagent + +[Term] +id: MS:1002783 +name: 6550 iFunnel Q-TOF LC/MS +def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002784 +name: 6550A iFunnel Q-TOF LC/MS +def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002785 +name: 6520B Q-TOF LC/MS +def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002786 +name: 6530A Q-TOF LC/MS +def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002787 +name: 6530B Q-TOF LC/MS +def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002788 +name: 6538 Q-TOF LC/MS +def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002789 +name: 6540 Q-TOF LC/MS +def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002790 +name: 6542 Q-TOF LC/MS +def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002791 +name: 6545 Q-TOF LC/MS +def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002792 +name: 6560 Q-TOF LC/MS +def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002793 +name: 6570 Q-TOF LC/MS +def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002794 +name: 6120B Quadrupole LC/MS +def: "The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002795 +name: 6150 Quadrupole LC/MS +def: "The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002796 +name: 6224 Time-of-Flight LC/MS +def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002797 +name: 6230A Time-of-Flight LC/MS +def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002798 +name: 6230B Time-of-Flight LC/MS +def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002799 +name: 6430 Triple Quadrupole LC/MS +def: "The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002800 +name: 6495A Triple Quadrupole LC/MS +def: "The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002801 +name: 6495B Triple Quadrupole LC/MS +def: "The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002802 +name: 7000A Triple Quadrupole GC/MS +def: "The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002803 +name: 7000B Triple Quadrupole GC/MS +def: "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002804 +name: 7800 Quadrupole ICP-MS +def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002805 +name: 8800 Triple Quadrupole ICP-MS +def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1002806 +name: ion +def: "Molecular entity having a net positive or negative electric charge." [PSI:MS] +is_a: MS:1000881 ! molecular entity + +[Term] +id: MS:1002807 +name: positive mode adduct ion +def: "Adduct ion with positive ionization." [PSI:MS] +is_a: MS:1000353 ! adduct ion + +[Term] +id: MS:1002808 +name: negative mode adduct ion +def: "Adduct ion with negative ionization." [PSI:MS] +is_a: MS:1000353 ! adduct ion + +[Term] +id: MS:1002809 +name: adduct ion attribute +def: "Nonphysical characteristic attributed to an adduct ion." [PSI:MS] +relationship: part_of MS:1000353 ! adduct ion + +[Term] +id: MS:1002810 +name: adduct ion X m/z +def: "Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [PSI:MS] +is_a: MS:1003056 ! adduct ion property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000040 ! m/z + +[Term] +id: MS:1002811 +name: adduct ion isotope +def: "Isotope of the matrix molecule M of an adduct formation." [PSI:MS] +is_a: MS:1003056 ! adduct ion property +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002812 +name: Regular expression for adduct ion formula +def: "(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." [PSI:PI] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1002813 +name: adduct ion formula +def: "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression." [PSI:MS] +is_a: MS:1002809 ! adduct ion attribute +relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]) +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002814 +name: volt-second per square centimeter +def: "An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]." [PSI:PI] +synonym: "Vs/cm^2" EXACT [] +is_a: UO:0000000 ! unit + +[Term] +id: MS:1002815 +name: inverse reduced ion mobility +def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units MS:1002814 ! volt-second per square centimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002816 +name: mean ion mobility array +def: "Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002817 +name: Bruker TDF format +def: "Bruker TDF raw file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002818 +name: Bruker TDF nativeID format +def: "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1002819 +name: Bruker TDF nativeID format, combined spectra +def: "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002820 +name: M+H ion +def: "Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton." [PSI:MS] +property_value: ionMass: "M + 1.007276" xsd:string +is_a: MS:1002807 ! positive mode adduct ion + +[Term] +id: MS:1002821 +name: M-H ion +def: "Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M." [PSI:MS] +property_value: ionMass: "M - 1.007276" xsd:string +is_a: MS:1002808 ! negative mode adduct ion + +[Term] +id: MS:1002822 +name: OpenMS file format +def: "File format developed by the OpenMS team." [PMID:27575624] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1002823 +name: idXML +def: "OpenMS intermediate identification format." [PSI:PI] +is_a: MS:1002822 ! OpenMS file format + +[Term] +id: MS:1002824 +name: featureXML +def: "OpenMS feature file format." [PSI:PI] +is_a: MS:1002822 ! OpenMS file format + +[Term] +id: MS:1002825 +name: consensusXML +def: "OpenMS consensus map format." [PSI:PI] +is_a: MS:1002822 ! OpenMS file format + +[Term] +id: MS:1002826 +name: MetaMorpheus +def: "MetaMorpheus search engine." [https://github.com/smith-chem-wisc/MetaMorpheus] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002827 +name: MetaMorpheus:score +def: "MetaMorpheus score for PSMs." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002828 +name: MetaMorpheus:protein score +def: "MetaMorpheus score for protein groups." [PSI:PI] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002829 +name: XCMS:into +def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002830 +name: XCMS:intf +def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002831 +name: XCMS:maxo +def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002832 +name: XCMS:area +def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI] +is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002833 +name: alternating polarity mode +def: "Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired." [PSI:PI] +is_a: MS:1000857 ! run attribute + +[Term] +id: MS:1002834 +name: ProteomeDiscoverer:Delta Score +def: "The Delta Score reported by Proteome Discoverer version 2." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002835 +name: LTQ Orbitrap Classic +def: "Thermo Fisher Scientific LTQ Orbitrap Classic." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002836 +name: iProX dataset identifier +def: "Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002837 +name: iProX dataset URI +def: "URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002838 +name: mzMLb format +def: "mzMLb file format, mzML encapsulated within HDF5." [PSI:PI, https://github.com/biospi/mzmlb] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002839 +name: Conversion to mzMLb +def: "Conversion of a file format to Proteomics Standards Initiative mzMLb file format." [PSI:PI] +is_a: MS:1000530 ! file format conversion + +[Term] +id: MS:1002840 +name: external reference data +def: "Data belonging to an external reference." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1002841 +name: external HDF5 dataset +def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the section of the BinaryDataArray." [PSI:PI] +is_a: MS:1002840 ! external reference data +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002842 +name: external offset +def: "The position in the external data where the array begins." [PSI:PI] +relationship: has_units UO:0000189 ! Count +is_a: MS:1002840 ! external reference data +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002843 +name: external array length +def: "Describes how many fields an array contains." [PSI:PI] +relationship: has_units UO:0000189 ! Count +is_a: MS:1002840 ! external reference data +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002844 +name: Experiment additional parameter +def: "Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam." [PSI:PI] +is_a: MS:1001458 ! spectrum generation information + +[Term] +id: MS:1002845 +name: Associated file URI +def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002846 +name: Associated raw file URI +def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002847 +name: ProteomeCentral dataset URI +def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002848 +name: Result file URI +def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002849 +name: Search engine output file URI +def: "URI of one search engine output file associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002850 +name: Peak list file URI +def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002851 +name: Other type file URI +def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002852 +name: Dataset FTP location +def: "FTP location of one entire PX data set." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002853 +name: Dataset with no associated published manuscript +def: "A dataset which does not have an associated published manuscript." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002854 +name: Peer-reviewed dataset +def: "Dataset has been peer-reviewed somehow." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002855 +name: Non peer-reviewed dataset +def: "Dataset that has not been peer-reviewed by any means." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002856 +name: Supported dataset by repository +def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002857 +name: Unsupported dataset by repository +def: "Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002858 +name: Dataset with its publication pending +def: "A dataset which has an associated manuscript pending for publication." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002859 +name: Additional associated raw file URI +def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002860 +name: Gel image file URI +def: "URI of one gel image file associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002861 +name: Reprocessed complete dataset +def: "All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002862 +name: Reprocessed subset dataset +def: "A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002863 +name: Data derived from previous dataset +def: "One dataset is a reanalysis of previously published data." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002864 +name: No PTMs are included in the dataset +def: "No post-translational-modifications are been included in the identified peptides of one dataset." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002865 +name: Accepted manuscript +def: "A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002866 +name: Reference +def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002867 +name: Experimental information has been refined since this experiment was originally made publicly available +def: "This means that the experimental information available has been improved, for instance precursor charges were added." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002868 +name: Original data +def: "One dataset is not a reanalysis of previously published data." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002869 +name: mzR +def: "Bioconductor package mzR for reading and writing mass spectrometry data files." [PSI:PI] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002870 +name: MSnbase +def: "Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data." [PMID:22113085] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002871 +name: CAMERA +def: "Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments." [PMID:22111785] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002872 +name: Panorama Public dataset identifier +def: "Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002873 +name: Panorama Public dataset URI +def: "URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002874 +name: TSQ Altis +def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002875 +name: TSQ Quantis +def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002876 +name: TSQ 9000 +def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002877 +name: Q Exactive HF-X +def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002878 +name: small molecule analysis software +def: "Software for the analysis of small molecules." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002879 +name: Progenesis QI +def: "Metabolomics analysis software for LC-MS data from Nonlinear Dynamics." [PSI:PI] +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1002880 +name: Compound Discoverer +def: "Metabolomics analysis software from Thermo Fisher Scientific." [PSI:PI] +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1002881 +name: MyCompoundID +def: "Metabolite identification tool MyCompoundID." [PSI:PI, PMID:23373753] +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1002882 +name: study variable average function +def: "Function used to calculate the study variable quantification value." [PSI:PI] +is_a: MS:1001184 ! search statistics + +[Term] +id: MS:1002883 +name: median +def: "Median function." [PSI:PI] +is_a: MS:1002882 ! study variable average function + +[Term] +id: MS:1002884 +name: study variable variation function +def: "Function used to calculate the study variable quantification variation value." [PSI:PI] +is_a: MS:1001184 ! search statistics + +[Term] +id: MS:1002885 +name: standard error +def: "Standard error function." [PSI:PI] +is_a: MS:1002884 ! study variable variation function + +[Term] +id: MS:1002886 +name: small molecule quantification datatype +def: "The value reported in a small molecule quantification." [PSI:PI] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002887 +name: Progenesis QI normalised abundance +def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI] +is_a: MS:1002886 ! small molecule quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002888 +name: small molecule confidence measure +def: "The confidence score produced by a small molecule analysis software." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002889 +name: Progenesis MetaScope score +def: "The confidence score produced by Progenesis QI." [PSI:PI] +is_a: MS:1002888 ! small molecule confidence measure +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002890 +name: fragmentation score +def: "The fragmentation confidence score." [PSI:PI] +is_a: MS:1002888 ! small molecule confidence measure +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002891 +name: isotopic fit score +def: "The isotopic fit confidence score." [PSI:PI] +is_a: MS:1002888 ! small molecule confidence measure +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002892 +name: ion mobility attribute +def: "An attribute describing ion mobility searches." [PSI:PI] +is_a: MS:1000503 ! scan attribute +is_a: MS:1002345 ! PSM-level attribute + +[Term] +id: MS:1002893 +name: ion mobility array +def: "Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided." [PSI:PI] +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1002894 +name: InChIKey +def: "Unique chemical structure identifier for chemical compounds." [PMID:273343401] +is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002895 +name: small molecule identification attribute +def: "Compound identification information." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002896 +name: compound identification confidence level +def: "Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461] +is_a: MS:1002895 ! small molecule identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002897 +name: isotopomer peak +def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] +comment: This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. +is_a: MS:1000231 ! peak +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002898 +name: Shimadzu Biotech QTOF nativeID format +def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:PI] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1002899 +name: msalign format +def: "msalign file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002900 +name: feature format +def: "TopFD feature file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002901 +name: TopPIC +def: "TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization." [PMID:27423895, http://proteomics.informatics.iupui.edu/software/toppic/index.html] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002902 +name: TopFD +def: "Top-down mass spectral feature detection." [http://proteomics.informatics.iupui.edu/software/toppic/index.html] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002903 +name: TopMG +def: "A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra." [PMID:28453668, http://proteomics.informatics.iupui.edu/software/topmg/index.html] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002904 +name: proteoform-level identification attribute +def: "Proteoform level information." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002905 +name: proteoform-level identification statistic +def: "Identification confidence metric for a proteoform." [PSI:PI] +is_a: MS:1002904 ! proteoform-level identification attribute + +[Term] +id: MS:1002906 +name: search engine specific score for proteoforms +def: "Search engine specific proteoform scores." [PSI:PI] +is_a: MS:1002905 ! proteoform-level identification statistic + +[Term] +id: MS:1002907 +name: proteoform-level global FDR +def: "Estimation of the global false discovery rate of proteoforms." [PSI:PI] +is_a: MS:1002905 ! proteoform-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002908 +name: proteoform-level local FDR +def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI] +is_a: MS:1002905 ! proteoform-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002909 +name: proteoform-level statistical threshold +def: "Estimated statistical threshold at proteoform-level." [PSI:PI] +is_a: MS:1002573 ! spectrum identification statistical threshold + +[Term] +id: MS:1002910 +name: proteoform-level global FDR threshold +def: "Threshold for the global false discovery rate of proteoforms." [PSI:PI] +is_a: MS:1002909 ! proteoform-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002911 +name: proteoform-level local FDR threshold +def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI] +is_a: MS:1002909 ! proteoform-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002912 +name: TopPIC input parameter +def: "Search engine input parameters specific to TopPIC." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002913 +name: TopPIC:fixed modification +def: "Fixed modifications for TopPIC searching." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter + +[Term] +id: MS:1002914 +name: TopPIC:N-term form +def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter + +[Term] +id: MS:1002915 +name: TopPIC:error tolerance +def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002916 +name: TopPIC:max shift +def: "Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002917 +name: TopPIC:min shift +def: "Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002918 +name: TopPIC:shift num +def: "Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002919 +name: TopPIC:spectral cutoff type +def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002920 +name: TopPIC:spectral cutoff value +def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002921 +name: TopPIC:proteoform-level cutoff type +def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002922 +name: TopPIC:proteoform-level cutoff value +def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002923 +name: TopPIC:generating function +def: "P-value and E-value estimation using generating function." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002924 +name: TopPIC:combined spectrum number +def: "Number of combined spectra." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002925 +name: TopPIC:mod file +def: "The text file containing the information of common PTMs." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter + +[Term] +id: MS:1002926 +name: TopPIC:thread number +def: "Number of threads used in TopPIC." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002927 +name: TopPIC:use TopFD feature +def: "Proteoform identification using TopFD feature file." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002928 +name: TopPIC:spectral E-value +def: "TopPIC spectrum-level E-value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002353 ! PSM-level e-value +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002929 +name: TopPIC:spectral FDR +def: "TopPIC spectrum-level FDR." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002351 ! PSM-level local FDR +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002930 +name: TopPIC:proteoform-level FDR +def: "TopPIC proteoform-level FDR." [PSI:PI] +is_a: MS:1002908 ! proteoform-level local FDR +is_a: MS:1002906 ! search engine specific score for proteoforms +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002931 +name: TopPIC:spectral p-value +def: "TopPIC spectrum-level p-value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002352 ! PSM-level p-value +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002932 +name: TopPIC:MIScore +def: "Modification identification score." [PMID:27291504] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002933 +name: TopPIC:MIScore threshold +def: "TopPIC:MIScore threshold." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002934 +name: TopMG input parameter +def: "Search engine input parameters specific to TopMG." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002935 +name: TopMG:fixed modification +def: "Fixed modifications for TopMG searching." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter + +[Term] +id: MS:1002936 +name: TopMG:N-term form +def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter + +[Term] +id: MS:1002937 +name: TopMG:error tolerance +def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002938 +name: TopMG:max shift +def: "Maximum value of the mass shift (in Dalton)." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002939 +name: TopMG:spectral cutoff type +def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002940 +name: TopMG:spectral cutoff value +def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002941 +name: TopMG:proteoform-level cutoff type +def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002942 +name: TopMG:proteoform-level cutoff value +def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002943 +name: TopMG:mod file +def: "The text file containing the information of common PTMs." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter + +[Term] +id: MS:1002944 +name: TopMG:thread number +def: "Number of threads used in TopMG." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002945 +name: TopMG:use TopFD feature +def: "Proteoform identification using TopFD feature file." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002946 +name: TopMG:proteoform graph gap size +def: "Gap size in constructing proteoform graph." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002947 +name: TopMG:variable PTM number +def: "Maximum number of variable PTMs." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002948 +name: TopMG:variable PTM number in proteoform graph gap +def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002949 +name: TopMG:use ASF-DIAGONAL +def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002950 +name: TopMG:spectral E-value +def: "TopMG spectrum-level E-value." [PSI:PI] +is_a: MS:1002353 ! PSM-level e-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002951 +name: TopMG:spectral FDR +def: "TopMG spectrum-level FDR." [PSI:PI] +is_a: MS:1002351 ! PSM-level local FDR +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002952 +name: TopMG:proteoform-level FDR +def: "TopMG proteoform-level FDR." [PSI:PI] +is_a: MS:1002908 ! proteoform-level local FDR +is_a: MS:1002906 ! search engine specific score for proteoforms +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002953 +name: TopMG:spectral p-value +def: "TopMG spectrum-level p-value." [PSI:PI] +is_a: MS:1002352 ! PSM-level p-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002954 +name: collisional cross sectional area +def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI] +is_a: MS:1000861 ! molecular entity property +relationship: has_units UO:0000324 ! square angstrom +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002955 +name: hr-ms compound identification confidence level +def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540] +is_a: MS:1002895 ! small molecule identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002956 +name: isotopic ion MS peak +def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI] +is_a: MS:1000231 ! peak +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002957 +name: isotopomer MS peak +def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI] +is_a: MS:1002956 ! isotopic ion MS peak +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002958 +name: isotopologue MS peak +def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI] +is_a: MS:1002956 ! isotopic ion MS peak +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002959 +name: isomer +def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] +is_a: MS:1000859 ! molecule +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002960 +name: isotopomer +def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html] +is_a: MS:1002959 ! isomer +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002961 +name: isotopologue +def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html] +is_a: MS:1002959 ! isomer +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002962 +name: mean +def: "The arithmetic mean." [PSI:PI] +is_a: MS:1002882 ! study variable average function + +[Term] +id: MS:1002963 +name: variation coefficient +def: "The coefficient of variation." [PSI:PI] +is_a: MS:1002884 ! study variable variation function + +[Term] +id: MS:1002964 +name: lipidomics analysis software +def: "Lipidomics analysis software." [PSI:PI] +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1002965 +name: Lipid Data Analyzer +def: "Lipid Data Analyzer software for lipid quantification." [PMID:29058722] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002966 +name: chrom format +def: "The Lipid Data Analyzer native chrom format." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002967 +name: LipidHunter +def: "Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets." [PMID:28753264] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002968 +name: LipidXplorer +def: "Software for consensual cross-platform lipidomics." [PMID:22272252] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002969 +name: LipidMatch +def: "An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data." [PMID:28693421] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002970 +name: Greazy +def: "Open-source software for automated phospholipid tandem mass spectrometry identification." [PMID:27186799] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002971 +name: LipidBlast +def: "LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library." [PMID:28660581] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002972 +name: Lipid-Pro +def: "A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms." [PMID:25433698] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002973 +name: LipidFinder +def: "A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets." [PMID:28405621] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002974 +name: LipiDex +def: "An integrated software package for high-confidence lipid identification." [PMID:29705063] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002975 +name: LIQUID +def: "An-open source software for identifying lipids in LC-MS/MS-based lipidomics data." [PMID:28158427] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002976 +name: ALEX +def: "Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1)." [PMID:24244551] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002977 +name: ALEX123 +def: "Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level." [PMID:29786091] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002978 +name: LIMSA +def: "Software tool for the quantitative analysis of mass spectrometric lipidome data." [PMID:17165823] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002979 +name: LOBSTAHS +def: "Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers." [PMID:27322848] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002980 +name: LipidQA +def: "Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species." [PMID:17720531] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002981 +name: Proline +def: "The Proline software suite for mass spectrometry based proteomics." [http://www.profiproteomics.fr/proline/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002982 +name: PepNovo +def: "PepNovo tool for de novo peptide sequencing." [PMID:15858974] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002983 +name: pNovo +def: "pNovo tool for de novo peptide sequencing and identification using HCD spectra." [PMID:20329752] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002984 +name: Novor +def: "Novor real-time peptide de novo sequencing software tool." [PMID:26122521] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002985 +name: in-gel digestion +def: "Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes." [PSI:PI] +is_a: MS:1000831 ! sample preparation + +[Term] +id: MS:1002986 +name: in-solution digestion +def: "Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes." [PSI:PI] +is_a: MS:1000831 ! sample preparation + +[Term] +id: MS:1002987 +name: IdentiPy +def: "IdentiPy." [PMID:29682971, https://bitbucket.org/levitsky/identipy] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002988 +name: IdentiPy:RHNS +def: "The IdentiPy result 'RHNS'." [PSI:PI] +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002989 +name: IdentiPy:hyperscore +def: "The IdentiPy result 'hyperscore'." [PSI:PI] +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002990 +name: ms_deisotope +def: "ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra." [https://github.com/mobiusklein/ms_deisotope] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002991 +name: python-psims +def: "python-psims, a library for generating mzML and mzIdentML." [https://github.com/mobiusklein/psims] +is_a: MS:1002333 ! conversion software + +[Term] +id: MS:1002995 +name: Andromeda:PEP +def: "Posterior error probability of the best identified peptide of the Andromeda search engine." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002996 +name: Andromeda:apl file format +def: "Peak list file format of the Andromeda search engine." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002997 +name: ProteomeXchange dataset identifier reanalysis number +def: "Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD)." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002998 +name: LCMS-9030 +def: "Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1002999 +name: LCMS-8060 +def: "Shimadzu Scientific Instruments LCMS-8060 MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003000 +name: LCMS-8050 +def: "Shimadzu Scientific Instruments LCMS-8050 MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003001 +name: LCMS-8045 +def: "Shimadzu Scientific Instruments LCMS-8045 MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003002 +name: LCMS-8040 +def: "Shimadzu Scientific Instruments LCMS-8040 MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003003 +name: LCMS-2020 +def: "Shimadzu Scientific Instruments LCMS-2020." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003004 +name: maXis II +def: "Bruker Daltonics' maXis II." [PSI:MS] +is_a: MS:1001547 ! Bruker Daltonics maXis series + +[Term] +id: MS:1003005 +name: timsTOF Pro +def: "Bruker Daltonics' timsTOF Pro." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003006 +name: mean inverse reduced ion mobility array +def: "Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units MS:1002814 ! volt-second per square centimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003007 +name: raw ion mobility array +def: "Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003008 +name: raw inverse reduced ion mobility array +def: "Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units MS:1002814 ! volt-second per square centimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003009 +name: Shimadzu Biotech LCD format +def: "Shimadzu Biotech LCD file format." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003010 +name: LPPtiger +def: "Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets." [PMID:29123162] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003011 +name: pFind +def: "Sequence-tag-based search engine pFind." [PMID:30295672] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003012 +name: KSDP score +def: "Kernel mass spectral dot product scoring function." [PMID:15044235] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better + +[Term] +id: MS:1003013 +name: i3tms +def: "i3-tms search engine and data-analysis software." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003014 +name: MSFragger +def: "A database search-based peptide identification tool." [PMID:28394336] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003015 +name: razor peptide +def: "Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides." [PSI:MS] +is_a: MS:1000860 ! peptide + +[Term] +id: MS:1003016 +name: ProteinProphet:peptide weight +def: "Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins." [PSI:PI] +is_a: MS:1002490 ! peptide-level scoring +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003017 +name: ProteinProphet:peptide group weight +def: "Fraction of peptide evidence attributable to a group of proteins." [PSI:PI] +is_a: MS:1002490 ! peptide-level scoring +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003018 +name: Philosopher +def: "General proteomics processing toolkit for shotgun proteomics." [https://philosopher.nesvilab.org/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003019 +name: pressure chromatogram +def: "Representation of chromatographic pressure versus time." [PSI:MS] +is_a: MS:1000626 ! chromatogram type + +[Term] +id: MS:1003020 +name: flow rate chromatogram +def: "Representation of the chromatographic flow rate versus time." [PSI:MS] +is_a: MS:1000626 ! chromatogram type + +[Term] +id: MS:1003021 +name: Fixed modification +def: "Post-translational modification which is assumed to be present at each instance of a residue type." [PSI:PI] +is_a: MS:1001055 ! modification parameters +is_a: MS:1003026 ! named element in mzIdentML + +[Term] +id: MS:1003022 +name: Variable modification +def: "Post-translational modification which may or may not be present at a residue type." [PSI:PI] +is_a: MS:1001055 ! modification parameters +is_a: MS:1003026 ! named element in mzIdentML + +[Term] +id: MS:1003023 +name: OpenPepXL +def: "Cross-Linking MS search engine." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1003024 +name: OpenPepXL:score +def: "The OpenPepXL score for a cross-link spectrum match." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003025 +name: named element +def: "A named element that is an attribute in a proteomics standards file." [PSI:PI] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1003026 +name: named element in mzIdentML +def: "A named element that is an attribute in a mzIdentML file." [PSI:PI] +is_a: MS:1003025 ! named element + +[Term] +id: MS:1003027 +name: named element in mzML +def: "A named element that is an attribute in a mzML file." [PSI:PI] +is_a: MS:1003025 ! named element + +[Term] +id: MS:1003028 +name: Orbitrap Exploris 480 +def: "Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003029 +name: Orbitrap Eclipse +def: "Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003030 +name: Mascot:MinNumSigUniqueSeqs +def: "Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1003031 +name: CPTAC accession number +def: "Main identifier of a CPTAC dataset." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003032 +name: compound identification confidence code in MS-DIAL +def: "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL] +is_a: MS:1002895 ! small molecule identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003033 +name: molecular entity attribute +def: "Non-inherent characteristic attributed to a molecular entity." [PSI:PI] +relationship: part_of MS:1000881 ! molecular entity + +[Term] +id: MS:1003034 +name: atom +def: "Smallest constituent unit of ordinary matter that constitutes a chemical element." [https://en.wikipedia.org/wiki/Atom] +is_a: MS:1000881 ! molecular entity + +[Term] +id: MS:1003035 +name: small molecule +def: "Low molecular weight (< 900 daltons) organic compound that may regulate a biological process." [https://en.wikipedia.org/wiki/Small_molecule] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1003036 +name: metabolite +def: "Small molecule that is the intermediate end product of metabolism." [https://en.wikipedia.org/wiki/Metabolite] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003037 +name: ribonucleotide +def: "Nucleotide containing ribose as its pentose component." [https://en.wikipedia.org/wiki/Ribonucleotide] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003038 +name: deoxyribonucleotide +def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [https://en.wikipedia.org/wiki/Deoxyribonucleotide] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003039 +name: amino acid +def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid." [https://en.wikipedia.org/wiki/Amino_acid] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003040 +name: monosaccharide +def: "Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule." [https://en.wikipedia.org/wiki/Monosaccharide] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003041 +name: nucleic acid +def: "Molecule composed of a chain of nucleotides." [https://en.wikipedia.org/wiki/Nucleic_acid] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1003042 +name: polysaccharide +def: "Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages." [https://en.wikipedia.org/wiki/Polysaccharide] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1003043 +name: number of residues +def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI] +is_a: MS:1000887 ! peptide attribute + +[Term] +id: MS:1003044 +name: number of missed cleavages +def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI] +is_a: MS:1000887 ! peptide attribute + +[Term] +id: MS:1003045 +name: peptide-to-protein mapping +def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI] +is_a: MS:1000887 ! peptide attribute + +[Term] +id: MS:1003046 +name: peptide-to-protein mapping attribute +def: "Nonphysical characteristic attributed to the result of peptide-to-protein mapping." [PSI:PI] +is_a: MS:1003045 ! peptide-to-protein mapping + +[Term] +id: MS:1003047 +name: protein sequence offset +def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI] +is_a: MS:1003046 ! peptide-to-protein mapping attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003048 +name: number of enzymatic termini +def: "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI] +is_a: MS:1003046 ! peptide-to-protein mapping attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003049 +name: peptidoform +def: "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." [PSI:PI] +is_a: MS:1000860 ! peptide + +[Term] +id: MS:1003050 +name: peptidoform attribute +def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI] +relationship: part_of MS:1003049 ! peptidoform + +[Term] +id: MS:1003051 +name: peptidoform ion +def: "Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI] +is_a: MS:1003049 ! peptidoform +synonym: "precursor" RELATED [] +synonym: "precursor ion" RELATED [] +synonym: "parent ion" RELATED [] + +[Term] +id: MS:1003052 +name: peptidoform ion property +def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI] +relationship: part_of MS:1003051 ! peptidoform ion + +[Term] +id: MS:1003053 +name: theoretical monoisotopic m/z +def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI] +is_a: MS:1003052 ! peptidoform ion property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003054 +name: theoretical average m/z +def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI] +is_a: MS:1003052 ! peptidoform ion property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003055 +name: adduct +def: "Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species." [https://en.wikipedia.org/wiki/Adduct] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1003056 +name: adduct ion property +def: "Physical measurable characteristic of an adduct ion." [PSI:PI] +relationship: part_of MS:1000353 ! adduct ion + +[Term] +id: MS:1003057 +name: scan number +def: "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI] +is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003058 +name: spectrum property +def: "Inherent or measurable characteristic of a spectrum." [PSI:PI] +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1003059 +name: number of peaks +def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003060 +name: number of data points +def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003061 +name: library spectrum name +def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI] +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term +synonym: "spectrum name" EXACT [] + +[Term] +id: MS:1003062 +name: library spectrum index +def: "Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0." [PSI:PI] +is_a: MS:1003234 ! library spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003063 +name: universal spectrum identifier +def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI] +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term +synonym: "USI" EXACT [] + +[Term] +id: MS:1003064 +name: spectrum aggregation attribute +def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] +is_a: MS:1000499 ! spectrum attribute + +[Term] +id: MS:1003065 +name: spectrum aggregation type +def: "Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] +is_a: MS:1003064 ! spectrum aggregation attribute + +[Term] +id: MS:1003066 +name: singleton spectrum +def: "Spectrum that is not the result of some aggregation process." [PSI:PI] +is_a: MS:1003065 ! spectrum aggregation type + +[Term] +id: MS:1003067 +name: consensus spectrum +def: "Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates." [PSI:PI] +is_a: MS:1003065 ! spectrum aggregation type + +[Term] +id: MS:1003068 +name: best replicate spectrum +def: "Spectrum that is considered the most representative from a pool of replicate spectra." [PSI:PI] +is_a: MS:1003065 ! spectrum aggregation type + +[Term] +id: MS:1003069 +name: number of replicate spectra available +def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI] +is_a: MS:1003064 ! spectrum aggregation attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003070 +name: number of replicate spectra used +def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI] +is_a: MS:1003064 ! spectrum aggregation attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003071 +name: spectrum origin attribute +def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] +is_a: MS:1000499 ! spectrum attribute + +[Term] +id: MS:1003072 +name: spectrum origin type +def: "Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI:PI] +is_a: MS:1003071 ! spectrum origin attribute + +[Term] +id: MS:1003073 +name: observed spectrum +def: "Spectrum that originates from an analysis attempt of a single analyte species on an instrument." [PSI:PI] +is_a: MS:1003072 ! spectrum origin type + +[Term] +id: MS:1003074 +name: predicted spectrum +def: "Spectrum that originates from a compututational algorithm that attempts to predict spectra." [PSI:PI] +is_a: MS:1003072 ! spectrum origin type + +[Term] +id: MS:1003075 +name: demultiplexed spectrum +def: "Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species." [PSI:PI] +is_a: MS:1003072 ! spectrum origin type + +[Term] +id: MS:1003076 +name: uninterpreted spectrum +def: "Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features." [PSI:PI] +is_a: MS:1000442 ! spectrum + +[Term] +id: MS:1003077 +name: interpreted spectrum +def: "Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature." [PSI:PI] +is_a: MS:1000442 ! spectrum + +[Term] +id: MS:1003078 +name: interpreted spectrum attribute +def: "Non-inherent characteristic attributed to an interpreted spectrum." [PSI:PI] +relationship: part_of MS:1003077 ! interpreted spectrum + +[Term] +id: MS:1003079 +name: total unassigned intensity fraction +def: "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003080 +name: top 20 peak unassigned intensity fraction +def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003081 +name: unidentified modification monoisotopic mass delta +def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the element in mzIdentML." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003082 +name: MS-DIAL +def: "Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors." [PMID:25938372] +is_a: MS:1002878 ! small molecule analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003083 +name: raw data file +def: "Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file)." [PSI:MS] +is_a: MS:1000577 ! source data file + +[Term] +id: MS:1003084 +name: processed data file +def: "File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument." [PSI:MS] +is_a: MS:1000577 ! source data file +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003085 +name: previous MSn-1 scan precursor intensity +def: "Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes." [PSI:MS] +is_a: MS:1001141 ! intensity of precursor ion +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003086 +name: precursor apex intensity +def: "Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope." [PSI:MS] +is_a: MS:1001141 ! intensity of precursor ion +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003087 +name: supported by repository but incomplete data and/or metadata +def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1003088 +name: truncation and zlib compression +def: "Data array compression using mantissa bit truncation followed by zlib compression." [https://github.com/biospi/pwiz] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1003089 +name: truncation, delta prediction and zlib compression +def: "Data array compression using mantissa bit truncation, delta prediction and zlib compression." [https://github.com/biospi/pwiz] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1003090 +name: truncation, linear prediction and zlib compression +def: "Data array compression using mantissa bit truncation, linear prediction and zlib compression." [https://github.com/biospi/pwiz] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1003091 +name: binary data compression parameter +def: "Settable parameter for a binary data compression event." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum +relationship: part_of MS:1000625 ! chromatogram + +[Term] +id: MS:1003092 +name: number of mantissa bits truncated +def: "Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI:MS] +is_a: MS:1003091 ! binary data compression parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1003093 +name: Lys-N +def: "Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues." [https://en.wikipedia.org/wiki/Lys-N] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001335 ! (?=K) + +[Term] +id: MS:1003094 +name: Orbitrap Exploris 240 +def: "Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003095 +name: Orbitrap Exploris 120 +def: "Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003096 +name: LTQ Orbitrap Velos Pro +def: "Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003097 +name: MaxQuant protein group-level score +def: "The probability based MaxQuant protein group score." [PSI:MS] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003098 +name: Andromeda peptide PEP +def: "Peptide probability from Andromeda." [PSI:MS] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003099 +name: MaxQuant-DIA peptide PEP +def: "Peptide probability from MaxQuant-DIA algorithm." [PSI:MS] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003100 +name: MaxQuant-DIA score +def: "PSM evidence score from MaxQuant-DIA algorithm." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003101 +name: MaxQuant-DIA PEP +def: "PSM evidence PEP probability from MaxQuant-DIA algorithm." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003102 +name: NIST msp comment +def: "Term for a comment field withing the NIST msp file format" [PSI:MS] +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003103 +name: ion annotation format +def: "Annotation format used for annotating individual spectrum ion peaks." [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute + +[Term] +id: MS:1003104 +name: peptide ion annotation format +def: "Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions." [PSI:MS] +is_a: MS:1003103 ! ion annotation format + +[Term] +id: MS:1003105 +name: cross-linked peptide ion annotation format +def: "Annotation format designed specifically for cross-linked peptide ion peaks." [PSI:MS] +is_a: MS:1003103 ! ion annotation format + +[Term] +id: MS:1003106 +name: glycan ion annotation format +def: "Annotation format designed specifically for glycan ion peaks." [PSI:MS] +is_a: MS:1003103 ! ion annotation format + +[Term] +id: MS:1003107 +name: lipid ion annotation format +def: "Annotation format designed specifically for lipid ion peaks." [PSI:MS] +is_a: MS:1003103 ! ion annotation format + +[Term] +id: MS:1003108 +name: PatternLab +def: "PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003109 +name: SIM-XL +def: "Identifying cross-linked peptides in complex protein mixtures" [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003110 +name: SIM-XL score +def: "SIM-XL identification search engine score" [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003111 +name: QUIN-XL +def: "Quantification of cross-linked peptides in complex protein mixtures" [PSI:MS] +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1003112 +name: Orbitrap ID-X +def: "Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003113 +name: OpenMS:ConsensusID PEP +def: "The OpenMS ConsesusID tool posterior error probability" [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003114 +name: OpenMS:Best PSM Score +def: "The score of the best PSM selected by the underlying identification tool" [PSI:MS] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003115 +name: OpenMS:Target-decoy PSM q-value +def: "The OpenMS Target-decoy q-values at PSM level" [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003116 +name: OpenMS:Target-decoy peptide q-value +def: "The OpenMS Target-decoy q-values at peptide sequence level" [PSI:MS] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003117 +name: OpenMS:Target-decoy protein q-value +def: "The OpenMS Target-decoy q-values at protein level" [PSI:MS] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003118 +name: EPIFANY +def: "A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework" [PSI:MS] +is_a: MS:1001456 ! analysis software +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1003119 +name: EPIFANY:Protein posterior probability +def: "Protein Posterior probability calculated by EPIFANY protein inference algorithm" [PSI:MS] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003120 +name: OpenMS:LFQ intensity +def: "The data type LFQ intensity produced by OpenMS." [PSI:MS] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003121 +name: OpenMS:LFQ spectral count +def: "The data type LFQ spectral count produced by OpenMS." [PSI:MS] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003122 +name: rapifleX +def: "Bruker Daltonics' rapiflex: MALDI TOF/TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1003123 +name: Bruker Daltonics timsTOF series +def: "Bruker Daltonics timsTOF series" [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1003124 +name: timsTOF fleX +def: "Bruker Daltonics' timsTOF fleX" [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003125 +name: ProSight:spectral Q-value +def: "ProSight spectrum-level Q-value." [PSI:MS] +is_a: MS:1002354 ! PSM-level q-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003126 +name: ProSight:spectral P-score +def: "ProSight spectrum-level P-score." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003127 +name: ProSight:spectral E-value +def: "ProSight spectrum-level E-value." [PSI:MS] +is_a: MS:1002353 ! PSM-level e-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003128 +name: ProSight:spectral C-score +def: "ProSight spectrum-level C-score." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003129 +name: proteoform-level Q-value +def: "Estimation of the Q-value for proteoforms." [PSI:MS] +is_a: MS:1002905 ! proteoform-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003130 +name: ProSight:proteoform Q-value +def: "ProSight proteoform-level Q-value." [PSI:MS] +is_a: MS:1003129 ! proteoform-level Q-value +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003131 +name: isoform-level identification attribute +def: "Isoform level information." [PSI:MS] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1003132 +name: isoform-level identification statistic +def: "Identification confidence metric for a isoform." [PSI:MS] +is_a: MS:1003131 ! isoform-level identification attribute + +[Term] +id: MS:1003133 +name: isoform-level Q-value +def: "Estimation of the Q-value for isoforms." [PSI:MS] +is_a: MS:1003132 ! isoform-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003134 +name: ProSight:isoform Q-value +def: "ProSight isoform-level Q-value." [PSI:MS] +is_a: MS:1003133 ! isoform-level Q-value +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003135 +name: ProSight:protein Q-value +def: "ProSight protein-level Q-value." [PSI:MS] +is_a: MS:1001869 ! protein-level q-value +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003136 +name: ProSight input parameter +def: "Search engine input parameters specific to ProSight." [PSI:MS] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1003137 +name: TDPortal input parameter +def: "Search engine input parameters specific to TDPortal." [PSI:MS] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1003138 +name: ProSight:Run delta m mode +def: "If true, runs delta m mode in ProSight." [PSI:MS] +is_a: MS:1003136 ! ProSight input parameter +is_a: MS:1003137 ! TDPortal input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1003139 +name: ProSight:Run Subsequence Search mode +def: "If true, runs Subsequence Search mode in ProSight." [PSI:MS] +is_a: MS:1003136 ! ProSight input parameter +is_a: MS:1003137 ! TDPortal input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1003140 +name: ProSight:Run Annotated Proteoform Search mode +def: "If true, runs Annotated Proteoform Search mode in ProSight." [PSI:MS] +is_a: MS:1003136 ! ProSight input parameter +is_a: MS:1003137 ! TDPortal input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1003141 +name: ProSight +def: "ProSight: Database search engine for top-down proteomics." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003142 +name: TDPortal +def: "TDPortal: Database search engine for top-down proteomics." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003143 +name: mass array +def: "A data array of mass values." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units UO:0000221 ! dalton + +[Term] +id: MS:1003144 +name: Triple Quad 7500 +def: "SCIEX Triple Quad 7500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1003145 +name: ThermoRawFileParser +def: "Cross-platform software to convert Thermo RAW files to a number of open formats." [DOI:10.1021/acs.jproteome.9b00328, PMID:31755270] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003146 +name: pyteomics +def: "Python module that helps handling various proteomics data analysis tasks." [DOI:10.1021/acs.jproteome.8b00717, PMID:30576148] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003147 +name: PTMProphet probability +def: "Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003148 +name: PTMProphet mean best probability +def: "PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003149 +name: PTMProphet normalized information content +def: " PTMProphet-computed PSM-specific normalized (0.0 – 1.0) measure of information content across all modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003150 +name: PTMProphet information content +def: " PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003151 +name: SHA-256 +def: "SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS] +is_a: MS:1000561 ! data file checksum type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003152 +name: GCMS-QP2010SE +def: "Shimadzu Scientific Instruments GCMS-QP2010SE." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003153 +name: raw ion mobility drift time array +def: "Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003154 +name: deconvoluted ion mobility array +def: "Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003155 +name: deconvoluted inverse reduced ion mobility array +def: "Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units MS:1002814 ! volt-second per square centimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003156 +name: deconvoluted ion mobility drift time array +def: "Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003157 +name: scanning quadrupole position lower bound m/z array +def: "Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] +is_a: MS:1000513 ! binary data array +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003158 +name: scanning quadrupole position upper bound m/z array +def: "Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] +is_a: MS:1000513 ! binary data array +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003159 +name: isolation window full range +def: "Indicates an acquisition mode in which the isolation window is a full range, rather than a subset of the full range." [PSI:MS] +is_a: MS:1000792 ! isolation window attribute + +[Term] +id: MS:1003160 +name: mzQC format +def: "Proteomics Standards Initiative mzQC format for quality control data." [PSI:MS] +is_a: MS:1003161 ! quality control data format + +[Term] +id: MS:1003161 +name: quality control data format +def: "Grouping term for quality control data formats." [PSI:MS] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1003162 +name: PTX-QC +def: "Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization." [DOI:10.1021/acs.jproteome.5b00780, PMID:26653327, https://github.com/cbielow/PTXQC/] +is_a: MS:1001456 ! analysis software +synonym: "PTXQC" EXACT [] + +[Term] +id: MS:1003163 +name: analyte mixture members +def: "The set of analyte identifiers that compose an interpretation of a spectrum." [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type MS:1002712 ! list of integers + +[Term] +id: MS:1003164 +name: QuaMeter IDFree +def: "QuaMeter IDFree software for QC metric calculation." [DOI:10.1021/ac4034455, PMID:24494671] +is_a: MS:1001456 ! analysis software +synonym: "QuaMeter" EXACT [] + +[Term] +id: MS:1003165 +name: iMonDB +def: "iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files." [DOI:10.1021/acs.jproteome.5b00127, PMID:25798920, https://github.com/bittremieux/iMonDB] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003166 +name: assigned intensity fraction +def: "Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum" [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003167 +name: MSn-1 isolation window precursor purity +def: "The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte" [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003168 +name: library spectrum comment +def: "A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools." [PSI:PI] +is_a: MS:1003234 ! library spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003169 +name: proforma peptidoform sequence +def: "Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation" [PSI:PI] +is_a: MS:1000889 ! peptidoform sequence +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003170 +name: spectral library +def: "A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments" [PSI:PI] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1003171 +name: spectral library attribute +def: "An attribute of a spectral library" [PSI:PI] +relationship: part_of MS:1003170 ! spectral library + +[Term] +id: MS:1003172 +name: library spectrum +def: "An entry in a spectral library representing a spectrum" [PSI:PI] +relationship: part_of MS:1003170 ! spectral library + +[Term] +id: MS:1003173 +name: numeric attribute +def: "An attribute that takes on a numeric value" [PSI:PI] +is_a: MS:1000547 ! object attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003174 +name: attribute maximum +def: "The maximum value for this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003175 +name: attribute minimum +def: "The minimum value for this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003176 +name: attribute mean +def: "The arithmetic mean value for this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003177 +name: attribute standard deviation +def: "The standard deviation (exact value of population, or estimate from sample) of this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003178 +name: attribute coefficient of variation +def: "The coefficient of variation of this attribute, i.e. standard deviation divided by the mean" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003179 +name: attribute summary value +def: "The most appropriate summary value of the attribute, usually but not necessarily the mean" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003180 +name: attribute median +def: "The median of this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003181 +name: combined dissociation method +def: "Combination of two or more dissociation methods that are known by a special term." [PSI:PI] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1003182 +name: electron-transfer/collision-induced dissociation +def: "Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID)." [PSI:PI] +synonym: "ETciD" EXACT [] +is_a: MS:1003181 ! combined dissociation method + +[Term] +id: MS:1003183 +name: Synapt XS +def: "Waters oa-ToF based Synapt XS." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003184 +name: SELECT SERIES Cyclic IMS +def: "Waters oa-ToF based SELECT SERIES Cyclic IMS." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003185 +name: SELECT SERIES MRT +def: "Waters oa-ToF based SELECT SERIES MRT." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003186 +name: library format version +def: "Version number of the [PSI] library format specification" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003187 +name: library identifier +def: "Short identifier for the library for easy reference, preferably but not necessarily globally unique" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003188 +name: library name +def: "A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library." [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003189 +name: library description +def: "Extended free-text description of the library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003190 +name: library version +def: "Version number of the library, usually refering to a certain release of a continually updated library " [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003191 +name: library URI +def: "URI or URL that uniquely identifies the library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003192 +name: decoy spectrum +def: "A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching" [PSI:PI] +is_a: MS:1003072 ! spectrum origin type + +[Term] +id: MS:1003193 +name: shuffle-and-reposition decoy spectrum +def: "A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence." [PSI:PI] +is_a: MS:1003192 ! decoy spectrum + +[Term] +id: MS:1003194 +name: precursor shift decoy spectrum +def: "A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum." [PSI:PI] +is_a: MS:1003192 ! decoy spectrum + +[Term] +id: MS:1003195 +name: unnatural peptidoform decoy spectrum +def: "A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform" [PSI:PI] +is_a: MS:1003192 ! decoy spectrum + +[Term] +id: MS:1003196 +name: unrelated species decoy spectrum +def: "A decoy spectrum that is a real spectrum of a naturally occuring peptidoform of an unrelated species that should not be found in the sample" [PSI:PI] +is_a: MS:1003192 ! decoy spectrum + +[Term] +id: MS:1003197 +name: license URI +def: "URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/)" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003198 +name: copyright notice +def: "Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003199 +name: change log +def: "Extended free-text description of the difference from the previous version" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003200 +name: software version +def: "Version number of the software package used for library creation" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003201 +name: library provenance attribute +def: "Abstract term containing several different types of provenance information" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003202 +name: BiblioSpec +def: "A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington" [PSI:PI] +is_a: MS:1001456 ! analysis software +is_a: MS:1003207 ! library creation software + +[Term] +id: MS:1003203 +name: constituent spectrum file +def: "Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible." [PSI:PI] +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003204 +name: constituent identification file +def: "Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible" [PSI:PI] +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003205 +name: constituent library file +def: "Source library URI which(at least) a subset of spectra were extracted from." [PSI:PI] +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003206 +name: library creation log +def: "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \n" [PSI:PI] +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003207 +name: library creation software +def: "Library creation software" [PSI:MS] +is_a: MS:1000531 ! software +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003208 +name: experimental precursor monoisotopic m/z +def: "The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003209 +name: monoisotopic m/z deviation +def: "The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum." [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003210 +name: average m/z deviation +def: "The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum." [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003211 +name: library spectrum attribute set +def: "A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003212 +name: library attribute set name +def: "A name to refer to a library attribute set" [PSI:PI] +relationship: part_of MS:1003211 ! library spectrum attribute set +relationship: part_of MS:1003238 ! library analyte attribute set +relationship: part_of MS:1003239 ! library interpretation attribute set +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003213 +name: mass spectrometry acquisition method +def: "Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS] +is_a: MS:1000524 ! data file content +is_a: MS:1001954 ! acquisition parameter + +[Term] +id: MS:1003214 +name: mass spectrometry acquisition method aspect +def: "Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS] +is_a: MS:1001458 ! spectrum generation information + +[Term] +id: MS:1003215 +name: data-independent acquisition +def: "Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions." [PSI:MS] +synonym: "DIA" EXACT [] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003216 +name: dissociation of full mass range +def: "Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003217 +name: dissociation of scanning quadrupole across a specified mass range +def: "Mass spectrometer data acquisition method wherein ????." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003218 +name: dissociation of sequential mass ranges +def: "Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003219 +name: ion mobility separation +def: "Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003220 +name: adduct deconvolution +def: "Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1003221 +name: data-dependent acquisition +def: "Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect +synonym: "DDA" EXACT [] + +[Term] +id: MS:1003222 +name: ion mobility deconvolution +def: "Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1003224 +name: data independent acquisition from dissociation of sequential mass ranges +def: "Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC." [PSI:MS] +is_a: MS:1003218 ! dissociation of sequential mass ranges +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003225 +name: data independent acquisition from dissociation of sequential mass ranges after ion mobility separation +def: "Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF." [PSI:MS] +is_a: MS:1003218 ! dissociation of sequential mass ranges +is_a: MS:1003219 ! ion mobility separation +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003226 +name: data independent acquisition from dissociation of full mass range after ion mobility separation +def: "Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF." [PSI:MS] +is_a: MS:1003216 ! dissociation of full mass range +is_a: MS:1003219 ! ion mobility separation +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003227 +name: data independent acquisition from dissociation of full mass range +def: "Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID." [PSI:MS] +is_a: MS:1003216 ! dissociation of full mass range +is_a: MS:1003219 ! ion mobility separation +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003228 +name: data independent acquisition from dissociation of scanning quadrupole across mass range +def: "Data independent mass spectrometer acquisition method wherein ???. An example of such an approach is Waters SONAR." [PSI:MS] +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003217 ! dissociation of scanning quadrupole across a specified mass range +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003229 +name: timsTOF +def: "Bruker Daltonics' timsTOF." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003230 +name: timsTOF Pro 2 +def: "Bruker Daltonics' timsTOF Pro 2." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003231 +name: timsTOF SCP +def: "Bruker Daltonics' timsTOF SCP." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003232 +name: PeakForest +def: "comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB)." [https://peakforest.org/] +is_a: MS:1001456 ! analysis software +is_a: MS:1003207 ! library creation software +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1003234 +name: library spectrum attribute +def: "An attribute that describes information about an entry in a spectral library" [PSI:PI] +relationship: part_of MS:1003172 ! library spectrum + +[Term] +id: MS:1003235 +name: paper spray ionization +def: "The ionization of analytes from a piece of paper by applying a solvent and voltage." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1003237 +name: library spectrum key +def: "An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library." [PSI:PI] +is_a: MS:1003234 ! library spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003238 +name: library analyte attribute set +def: "A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003239 +name: library interpretation attribute set +def: "A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003240 +name: peak intensity transform +def: "A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores" [PSI:PI] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1003241 +name: square root transform +def: "A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots" [PSI:PI] +is_a: MS:1003240 ! peak intensity transform + +[Term] +id: MS:1003242 +name: rank transform +def: "A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks" [PSI:PI] +is_a: MS:1003240 ! peak intensity transform + +[Term] +id: MS:1003243 +name: adduct ion mass +def: "The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule’s mass plus the mass of a proton)" [PSI:PI] +is_a: MS:1003056 ! adduct ion property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003244 +name: peptide accession number +def: "Accession number (e.g. in PeptideAtlas) of the peptide sequence" [PSI:PI] +is_a: MS:1003050 ! peptidoform attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003245 +name: Q Exactive UHMR +def: "Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003246 +name: ultraviolet photodissociation +def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons." [PSI:MS] +synonym: "UVPD" EXACT [] +is_a: MS:1000435 ! photodissociation + +[Term] +id: MS:1003247 +name: negative electron transfer dissociation +def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation." [DOI:10.1016/j.jasms.2005.01.015, PSI:MS] +synonym: "NETD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1003248 +name: proton transfer reaction +def: "Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation." [DOI:10.1002/mas.20048, PSI:MS] +synonym: "PTR" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1003249 +name: proton transfer charge reduction +def: "Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte." [PSI:MS] +synonym: "PTCR" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1003250 +name: count of identified peptidoforms +def: "The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] +is_a: MS:1002702 ! peptide sequence-level result list attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1003251 +name: count of identified spectra +def: "The number of spectra that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] +is_a: MS:1002700 ! PSM-level result list attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1003252 +name: Xevo G2-XS QTof +def: "Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003253 +name: DIA-NN +def: "A universal software for data-independent acquisition (DIA) proteomics data processing" [PMID:31768060, https://github.com/vdemichev/DiaNN] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003254 +name: peak attribute +def: "An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. " [PSI:PI] +relationship: part_of MS:1000231 ! peak + +[Term] +id: MS:1003255 +name: pre-decharged charge state +def: "For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. " [PSI:PI] +is_a: MS:1003254 ! peak attribute + +[Term] +id: MS:1003256 +name: peptidoform ion attribute +def: "Non-inherent characteristic attributed to a peptidoform" [PSI:PI] +relationship: part_of MS:1003051 ! peptidoform ion + +[Term] +id: MS:1003257 +name: library spectrum cross reference +def: "A link from one spectrum to another spectrum of interest " [PSI:PI] +is_a: MS:1003234 ! library spectrum attribute + +[Term] +id: MS:1003258 +name: related spectrum +def: "A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. " [PSI:PI] +is_a: MS:1003257 ! library spectrum cross reference + +[Term] +id: MS:1003259 +name: related spectrum keys +def: "A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. " [PSI:PI] +is_a: MS:1003258 ! related spectrum +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term + +[Term] +id: MS:1003260 +name: related spectrum USI +def: "A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI] +is_a: MS:1003258 ! related spectrum +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003261 +name: related spectrum description +def: "A free-text string describing the related spectrum and/or its relationship to this spectrum" [PSI:PI] +relationship: part_of MS:1003258 ! related spectrum +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003262 +name: similar spectrum +def: "A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion." [PSI:PI] +is_a: MS:1003257 ! library spectrum cross reference + +[Term] +id: MS:1003263 +name: similar spectrum keys +def: "A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. " [PSI:PI] +is_a: MS:1003262 ! similar spectrum +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term + +[Term] +id: MS:1003264 +name: similar spectrum USI +def: "A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI] +is_a: MS:1003262 ! similar spectrum +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003265 +name: spectrum cluster +def: "A group of spectra that are spectrally similar to each other" [PSI:PI] +relationship: part_of MS:1003170 ! spectral library + +[Term] +id: MS:1003266 +name: spectrum cluster attribute +def: "A non-inherent characteristic of a spectrum cluster" [PSI:PI] +relationship: part_of MS:1003265 ! spectrum cluster + +[Term] +id: MS:1003267 +name: spectrum cluster key +def: "An ordinal number uniquely identifying a spectrum cluster. It should start with 1." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003268 +name: spectrum cluster member spectrum keys +def: "A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term + +[Term] +id: MS:1003269 +name: spectrum cluster member USI +def: "A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003270 +name: proforma peptidoform ion notation +def: "A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type." [PSI:PI] +is_a: MS:1003256 ! peptidoform ion attribute + +[Term] +id: MS:1003271 +name: peak annotation +def: "The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum." [PSI:PI] +relationship: part_of MS:1000231 ! peak + +[Term] +id: MS:1003272 +name: peak annotation string +def: "A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'." [PSI:PI] +relationship: part_of MS:1003271 ! peak annotation +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003273 +name: peak annotation confidence +def: "A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'." [PSI:PI] +relationship: part_of MS:1003271 ! peak annotation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003274 +name: peak annotation confidence metric +def: "A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1." [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute + +[Term] +id: MS:1003275 +name: other attribute name +def: "A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value" [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute + +[Term] +id: MS:1003276 +name: other attribute value +def: "A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name" [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute + +[Term] +id: MS:1003277 +name: value between -1 and 1 inclusive +def: "Value range for signed normalized score values." [PSI:PI] +is_a: MS:1002304 ! domain range + +[Term] +id: MS:1003278 +name: m/z variability of peak +def: "A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003254 ! peak attribute + +[Term] +id: MS:1003279 +name: observation frequency of peak +def: "The frequency at which this peak is observed among replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003254 ! peak attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003280 +name: intensity variability of peak +def: "A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003254 ! peak attribute + +[Term] +id: MS:1003281 +name: Casanovo +def: "Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/." [https://github.com/Noble-Lab/casanovo/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003282 +name: Bruker TSF format +def: "Bruker TSF raw file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003283 +name: Bruker TSF nativeID format +def: "Native format defined by frame=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1003284 +name: Bruker TSF nativeID format, combined spectra +def: "Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + + +[Term] +id: MS:1003285 +name: standard deviation of m/z values of peak among replicates +def: "The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003278 ! m/z variability of peak +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003286 +name: coefficient of variation of intensity of peak among replicates +def: "The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003280 ! intensity variability of peak +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003287 +name: standard deviation of intensity of peak among replicates +def: "The standard deviation of the intensities of this peak among the replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003280 ! intensity variability of peak +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003288 +name: number of unassigned peaks +def: "The number of unassigned peaks in the spectrum." [NIST] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003289 +name: intensity of highest unassigned peak +def: "The intensity of the highest unassigned peak in the spectrum." [NIST] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003290 +name: number of unassigned peaks among top 20 peaks +def: "The number of unassigned peaks among the most intense 20 peaks in the spectrum." [NIST] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003291 +name: Luciphor deltaScore +def: "Luciphor phosphosite localization score" [PSI:MS] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003292 +name: TSQ Altis Plus +def: "Thermo Scientific TSQ Altis Plus Triple Quadrupole MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003293 +name: ZenoTOF 7600 +def: "SCIEX ZenoTOF 7600." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1003294 +name: electron activated dissociation +def: "A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins." [PSI:MS] +synonym: "EAD" EXACT [] +is_a: MS:1000250 ! electron capture dissociation + +[Term] +id: MS:4000000 +name: PSI-MS CV Quality Control Vocabulary +def: "PSI Quality Control controlled vocabulary term." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:4000001 +name: QC metric +def: "Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations." [PSI:MS] +relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary + +[Term] +id: MS:4000002 +name: QC metric value type +def: "The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix." [PSI:MS] +relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary + +[Term] +id: MS:4000003 +name: single value +def: "Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value)." [PSI:MS] +is_a: MS:4000002 ! QC metric value type + +[Term] +id: MS:4000004 +name: n-tuple +def: "Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable)." [PSI:MS] +is_a: MS:4000002 ! QC metric value type + +[Term] +id: MS:4000005 +name: table +def: "Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value)." [PSI:MS] +comment: The actual structure of the table is defined in the mzQC specification document. In short: it must have at least one column, and MAY have optional columns. +is_a: MS:4000002 ! QC metric value type + +[Term] +id: MS:4000006 +name: matrix +def: "A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable)." [PSI:MS] +comment: The actual structure of the matrix is defined in the mzQC specification document. +is_a: MS:4000002 ! QC metric value type + +[Term] +id: MS:4000007 +name: QC metric category +def: "Categorization of the QC metric." [PSI:MS] +relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary + +[Term] +id: MS:4000008 +name: ID based metric +def: "QC metric based on identification results." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000009 +name: ID free metric +def: "QC metric not based on identification results." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000010 +name: quantification based metric +def: "QC metric based on quantification results." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000012 +name: single run based metric +def: "QC metric calculated from a single run (e.g. one .raw file)." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000013 +name: multiple runs based metric +def: "QC metric calculated from multiple runs (e.g. multiple .raw files)." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000014 +name: single spectrum based metric +def: "QC metric calculated from a single spectrum." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000015 +name: multiple spectra based metric +def: "QC metric calculated from multiple spectra." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000016 +name: retention time metric +def: "QC metric related to retention time." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000017 +name: chromatogram metric +def: "QC metric related to a chromatogram." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000018 +name: XIC metric +def: "QC metric related to an extracted ion chromatogram." [PSI:MS] +is_a: MS:4000017 ! chromatogram metric + +[Term] +id: MS:4000019 +name: MS metric +def: "QC metric related to the mass spectrometry acquisition." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000020 +name: ion source metric +def: "QC metric related to events in the ion source." [PSI:MS] +is_a: MS:4000019 ! MS metric + +[Term] +id: MS:4000021 +name: MS1 metric +def: "QC metric based on MS1 events." [PSI:MS] +is_a: MS:4000019 ! MS metric + +[Term] +id: MS:4000022 +name: MS2 metric +def: "QC metric based on MS2 events." [PSI:MS] +is_a: MS:4000019 ! MS metric + +[Term] +id: MS:4000023 +name: sample preparation metric +def: "QC metric related to the sample preparation." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000024 +name: environment metric +def: "QC metric related to measurements of the ambient environment, such as the laboratory." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000050 +name: XIC50 fraction +def: "The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC." [PSI:MS] +comment: This metric characterises the distribution of precursor peak widths, much as the N50 characterises contig sizes in genome assembly. +synonym: "XIC-WideFrac" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept UO:0000191 ! fraction + +[Term] +id: MS:4000051 +name: XIC-FWHM quantiles +def: "The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of of XIC-FWHM-Q1,Q2,Q3." [PSI:MS] +synonym: "XIC-FWHM-Q1" RELATED [PMID:24494671] +synonym: "XIC-FWHM-Q2" RELATED [PMID:24494671] +synonym: "XIC-FWHM-Q3" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000018 ! XIC metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept MS:1000086 ! full width at half-maximum +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_units UO:0000010 ! second + +[Term] +id: MS:4000052 +name: XIC-Height quartile ratios +def: "The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3." [PSI:MS] +synonym: "XIC-Height-Q2" RELATED [PMID:24494671] +synonym: "XIC-Height-Q3" RELATED [PMID:24494671] +synonym: "XIC-Height-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000018 ! XIC metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept STATO:0000105 ! log signal intensity ratio +relationship: has_value_concept UO:0000191 ! fraction + +[Term] +id: MS:4000053 +name: chromatography duration +def: "The retention time duration of the chromatography in seconds." [PSI:MS] +synonym: "RT-Duration" RELATED [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept NCIT:C25330 ! Duration +relationship: has_units UO:0000010 ! second + +[Term] +id: MS:4000054 +name: TIC quarters RT fraction +def: "The interval when the respective quarter of the TIC accumulates divided by retention time duration." [PSI:QC] +synonym: "RT-TIC-Q1" RELATED [PMID:24494671] +synonym: "RT-TIC-Q2" RELATED [PMID:24494671] +synonym: "RT-TIC-Q3" RELATED [PMID:24494671] +synonym: "RT-TIC-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000191 ! fraction + +[Term] +id: MS:4000055 +name: MS1 quarter RT fraction +def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration." [PSI:QC] +synonym: "RT-MS-Q1" RELATED [PMID:24494671] +synonym: "RT-MS-Q2" RELATED [PMID:24494671] +synonym: "RT-MS-Q3" RELATED [PMID:24494671] +synonym: "RT-MS-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000191 ! fraction + +[Term] +id: MS:4000056 +name: MS2 quarter RT fraction +def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration." [PSI:QC] +synonym: "RT-MSMS-Q1" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q2" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q3" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000191 ! fraction + +[Term] +id: MS:4000057 +name: MS1 TIC-change quartile ratios +def: "The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3" [PSI:MS] +synonym: "MS1-TIC-Change-Q2" RELATED [PMID:24494671] +synonym: "MS1-TIC-Change-Q3" RELATED [PMID:24494671] +synonym: "MS1-TIC-Change-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept STATO:0000105 ! log signal intensity ratio + +[Term] +id: MS:4000058 +name: MS1 TIC quartile ratios +def: "The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3." [PSI:MS] +synonym: "MS1-TIC-Q2" RELATED [PMID:24494671] +synonym: "MS1-TIC-Q3" RELATED [PMID:24494671] +synonym: "MS1-TIC-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept STATO:0000105 ! log signal intensity ratio + +[Term] +id: MS:4000059 +name: number of MS1 spectra +def: "The number of MS1 events in the run." [PSI:MS] +synonym: "MS1-Count" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000060 +name: number of MS2 spectra +def: "The number of MS2 events in the run." [PSI:MS] +synonym: "MS2-Count" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000061 +name: MS1 density quantiles +def: "The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode." [PSI:MS] +synonym: "MS1-Density-Q1" RELATED [PMID:24494671] +synonym: "MS1-Density-Q2" RELATED [PMID:24494671] +synonym: "MS1-Density-Q3" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_concept NCIT:C45781 ! Density +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000062 +name: MS2 density quantiles +def: "The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode." [PSI:MS] +synonym: "MS2-Density-Q1" RELATED [PMID:24494671] +synonym: "MS2-Density-Q2" RELATED [PMID:24494671] +synonym: "MS2-Density-Q3" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_concept NCIT:C45781 ! Density +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000063 +name: MS2 known precursor charges fractions +def: "The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher." [PSI:MS] +synonym: "MS2-PrecZ-1" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-2" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-3" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-4" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-5" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-more" NARROW [PMID:24494671] +synonym: "IS-3A" RELATED [PMID:19837981] +synonym: "IS-3B" RELATED [PMID:19837981] +synonym: "IS-3C" RELATED [PMID:19837981] +comment: the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2. +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_column MS:1000041 ! charge state +relationship: has_column UO:0000191 ! fraction + +[Term] +id: MS:4000064 +name: MS2 unknown and likely precursor charges fractions +def: "The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states." [PSI:MS] +synonym: "MS2-PrecZ-likely-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-likely-multi" RELATED [PMID:24494671] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_column MS:1000041 ! charge state +relationship: has_column UO:0000191 ! fraction + +[Term] +id: MS:4000065 +name: fastest frequency for MS level 1 collection +def: "Fastest frequency for MS level 1 collection" [PSI:MS] +comment: Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. +synonym: "MS1-Freq-Max" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000106 ! hertz + +[Term] +id: MS:4000066 +name: fastest frequency for MS level 2 collection +def: "Fastest frequency for MS level 2 collection" [PSI:MS] +comment: Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. +synonym: "MS2-Freq-Max" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000106 ! hertz + +[Term] +id: MS:4000067 +name: MS run duration +def: "The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000019 ! MS metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept NCIT:C25330 ! Duration +relationship: has_units UO:0000010 ! second + +[Term] +id: MS:4000068 +name: spectra half-TIC +def: "The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_optional_column MS:1003063 ! universal spectrum identifier +relationship: has_optional_column MS:1000767 ! native spectrum identifier format +relationship: has_column UO:0000191 ! fraction +relationship: has_relation MS:1000285 ! total ion current + +[Term] +id: MS:4000069 +name: m/z acquisition range +def: "Upper and lower limit of m/z precursor values at which MSn spectra are recorded." [PSI:MS] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000019 ! MS metric +relationship: has_units MS:1000040 ! m/z +relationship: has_value_concept STATO:0000035 ! range + +[Term] +id: MS:4000070 +name: retention time acquisition range +def: "Upper and lower limit of retention time at which spectra are recorded." [PSI:MS] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_units UO:0000010 ! second +relationship: has_value_concept STATO:0000035 ! range + +[Term] +id: MS:4000071 +name: number of chromatograms +def: "The number of chromatograms recorded for the run." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000072 +name: observed mass accuracy +def: "Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum." [PSI:MS] +relationship: has_metric_category MS:4000014 ! single spectrum based metric +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_concept MS:1000014 ! accuracy + +[Term] +id: MS:4000073 +name: QC sample metric +def: "A QC metric based on a QC sample of known content." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000074 +name: high complexity QC sample metric +def: "A QC metric based on a QC sample of known and high complexity content." [PSI:MS] +is_a: MS:4000073 ! QC sample metric + +[Term] +id: MS:4000075 +name: low complexity QC sample metric +def: "A QC metric based on a QC sample of known and low complexity content." [PSI:MS] +is_a: MS:4000073 ! QC sample metric + +[Term] +id: MS:4000076 +name: QC2 sample metric +def: "A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design." [PSI:MS, PMID:23088386, PMID:29324744] +comment: Expected peptides from QC2 sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR' +is_a: MS:4000074 ! high complexity QC sample metric + +[Term] +id: MS:4000077 +name: QC1 sample metric +def: "A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design)." [PSI:MS, PMID:23088386, PMID:29324744] +comment: Expected peptides from QC1 sample measurement are: 'LVNELTEFAK','HLVDEPQNLIK','VPQVSTPTLVEVSR','EAC(Carbamidomethyl)FAVEGPK','EYEATLEEC(Carbamidomethyl)C(Carbamidomethyl)AK','EC(Carbamidomethyl)C(Carbamidomethyl)HGDLLEC(Carbamidomethyl)ADDR','SLHTLFGDELC(Carbamidomethyl)K','TC(Carbamidomethyl)VADESHAGC(Carbamidomethyl)EK','YIC(Carbamidomethyl)DNQDTISSK','NEC(Carbamidomethyl)FLSHK' +is_a: MS:4000075 ! low complexity QC sample metric + +[Term] +id: MS:4000078 +name: QC2 sample mass accuracies +def: "Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000076 ! QC2 sample metric +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_column MS:1003169 ! proforma peptidoform sequence +relationship: has_column MS:4000072 ! observed mass accuracy + +[Term] +id: MS:4000079 +name: QC2 sample intensities +def: "Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000076 ! QC2 sample metric +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_column MS:1003169 ! proforma peptidoform sequence +relationship: has_optional_column MS:1001858 ! XIC area +relationship: has_optional_column MS:1001859 ! normalized XIC area +relationship: has_optional_column MS:1001844 ! MS1 feature area +relationship: has_optional_column MS:1001843 ! MS1 feature maximum intensity +relationship: has_optional_column MS:1003085 ! previous MSn-1 scan precursor intensity + +[Term] +id: MS:4000080 +name: QC non-metric term +def: "QC terms associated but not directly metrics themselves." [PSI:MS] +relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary + +[Term] +id: MS:4000081 +name: first principal component +def: "Data from the first principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "1st PC" EXACT [] + +[Term] +id: MS:4000082 +name: second principal component +def: "Data from the second principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "2nd PC" EXACT [] + +[Term] +id: MS:4000083 +name: third principal component +def: "Data from the third principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "3rd PC" EXACT [] + +[Term] +id: MS:4000084 +name: fourth principal component +def: "Data from the fourth principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "4th PC" EXACT [] + +[Term] +id: MS:4000085 +name: fifth principal component +def: "Data from the fifth principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "5th PC" EXACT [] + +[Term] +id: MS:4000086 +name: mzQC input reference +def: "Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:4000087 +name: mzQC plot label +def: "Used to supply alternative labels for plotting figures." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:4000088 +name: batch label +def: "Used to supply batch label information with any string value." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:4000089 +name: injection sequence label +def: "Used to supply injection sequence information with consecutive whole numbers." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:4000090 +name: principal component analysis of MaxQuant's protein group raw intensities +def: "A table with the PCA results of MaxQuant's protein group raw intensities." [PSI:MS] {http://coxdocs.org/doku.php?id="maxquant:table:directory&s[]=output"} +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component + +[Term] +id: MS:4000091 +name: principal component analysis of MaxQuant's protein group lfq intensities +def: "A table with the PCA results of MaxQuant's protein group lfq intensities." [PSI:MS] {http://coxdocs.org/doku.php?id="maxquant:table:directory&s[]=output"} +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component + +[Term] +id: MS:4000092 +name: identified MS1 feature area principal component analysis result +def: "A table with the PCA results of identified MS1 feature areas." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component +relationship: has_optional_column MS:4000087 ! mzQC plot label +relationship: has_optional_column MS:4000088 ! batch label +relationship: has_optional_column MS:4000089 ! injection sequence label + +[Term] +id: MS:4000093 +name: unidentified MS1 feature area principal component analysis result +def: "A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component +relationship: has_optional_column MS:4000087 ! mzQC plot label +relationship: has_optional_column MS:4000088 ! batch label +relationship: has_optional_column MS:4000089 ! injection sequence label + +[Term] +id: MS:4000094 +name: batch-corrected identified MS1 feature area principal component analysis result +def: "A table with the PCA results of identified MS1 feature areas after batch-correction." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component +relationship: has_optional_column MS:4000087 ! mzQC plot label +relationship: has_optional_column MS:4000088 ! batch label +relationship: has_optional_column MS:4000089 ! injection sequence label + +[Term] +id: PEFF:0000001 +name: PEFF CV term +def: "PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: PEFF:0000002 +name: PEFF file header section term +def: "CV term that may appear in a PEFF file header section." [PSI:PEFF] +is_a: PEFF:0000001 ! PEFF CV term + +[Term] +id: PEFF:0000003 +name: PEFF file sequence entry term +def: "CV term that may appear in a description line of a PEFF file individual sequence entry." [PSI:PEFF] +is_a: PEFF:0000001 ! PEFF CV term + +[Term] +id: PEFF:0000008 +name: DbName +def: "PEFF keyword for the sequence database name." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000009 +name: Prefix +def: "PEFF keyword for the sequence database prefix." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000010 +name: DbDescription +def: "PEFF keyword for the sequence database short description." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000011 +name: Decoy +def: "PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000012 +name: DbSource +def: "PEFF keyword for the source of the database file." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000013 +name: DbVersion +def: "PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000014 +name: DbDate +def: "OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider." [PSI:PEFF] +comment: This term was obsoleted. +is_a: PEFF:0000002 ! PEFF file header section term +is_obsolete: true + +[Term] +id: PEFF:0000015 +name: NumberOfEntries +def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000016 +name: Conversion +def: "PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000017 +name: SequenceType +def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_regexp PEFF:1002002 ! regular expression for PEFF molecular sequence type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000018 +name: SpecificKey +def: "PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000019 +name: SpecificValue +def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000020 +name: DatabaseDescription +def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000021 +name: GeneralComment +def: "PEFF keyword for a general comment." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000022 +name: ProteoformDb +def: "PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000023 +name: OptionalTagDef +def: "PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000024 +name: HasAnnotationIdentifiers +def: "PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001001 +name: DbUniqueId +def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF] +comment: This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant. +is_a: PEFF:0000003 ! PEFF file sequence entry term +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001002 +name: PName +def: "PEFF keyword for the protein full name." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001003 +name: NcbiTaxId +def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001004 +name: TaxName +def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001005 +name: GName +def: "PEFF keyword for the gene name." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001006 +name: Length +def: "PEFF keyword for the sequence length." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001007 +name: SV +def: "PEFF keyword for the sequence version." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001008 +name: EV +def: "PEFF keyword for the entry version." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001009 +name: PE +def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001010 +name: Processed +def: "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001011 +name: Variant +def: "OBSOLETE Sequence variation (substitution, insertion, deletion)." [PSI:PEFF] +comment: This term was made obsolete in favor of VariantSimple and VariantComplex. +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001012 +name: ModResPsi +def: "PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001013 +name: ModRes +def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001014 +name: AltAC +def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001015 +name: SeqStatus +def: "PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002003 ! regular expression for PEFF sequence status +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001016 +name: CC +def: "PEFF keyword for the entry associated comment." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001017 +name: KW +def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001018 +name: GO +def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001019 +name: XRef +def: "PEFF keyword for the cross-reference to an external resource." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001020 +name: mature protein +def: "Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001021 +name: signal peptide +def: "Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001022 +name: transit peptide +def: "Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001023 +name: Conflict +def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001024 +name: Crc64 +def: "PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001025 +name: Domain +def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001026 +name: ID +def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001027 +name: ModResUnimod +def: "PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001028 +name: VariantSimple +def: "PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001029 +name: VariantComplex +def: "PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001030 +name: Proteoform +def: "PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001031 +name: DisulfideBond +def: "PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001032 +name: PEFF molecule processing keyword +def: "PEFF keyword describing the type of processing event being described." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term + +[Term] +id: PEFF:0001033 +name: Comment +def: "PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001034 +name: propeptide +def: "Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001035 +name: initiator methionine +def: "N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:1002001 +name: regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +def: "([0-9]+|[A-Z*](|.+)?)." [PSI:PEFF] +is_a: MS:1002479 ! regular expression + +[Term] +id: PEFF:1002002 +name: regular expression for PEFF molecular sequence type +def: "(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." [PSI:PEFF] +is_a: MS:1002479 ! regular expression + +[Term] +id: PEFF:1002003 +name: regular expression for PEFF sequence status +def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF] +is_a: MS:1002479 ! regular expression + + +[Term] +id: UO:0000000 +name: unit +namespace: unit.ontology +def: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] +created_by: george gkoutos + +[Term] +id: UO:0000001 +name: length unit +namespace: unit.ontology +def: "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001708 +created_by: george gkoutos + +[Term] +id: UO:0000002 +name: mass unit +namespace: unit.ontology +def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0000125 +relationship: is_unit_of PATO:0000128 +created_by: george gkoutos + +[Term] +id: UO:0000003 +name: time unit +namespace: unit.ontology +alt_id: UO:0000149 +def: "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] +subset: unit_group_slim +synonym: "time derived unit" EXACT [] +is_a: UO:0000000 +relationship: is_unit_of PATO:0000165 +relationship: is_unit_of PATO:0001309 +created_by: george gkoutos + +[Term] +id: UO:0000005 +name: temperature unit +namespace: unit.ontology +alt_id: UO:0000126 +def: "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] +subset: unit_group_slim +synonym: "temperature derived unit" EXACT [] +is_a: UO:0000000 +relationship: is_unit_of PATO:0000146 +created_by: george gkoutos + +[Term] +id: UO:0000008 +name: meter +namespace: unit.ontology +def: "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST] +subset: unit_slim +synonym: "m" EXACT [] +synonym: "metre" EXACT [] +is_a: UO:0000001 +is_a: UO:0000045 +created_by: george gkoutos + +[Term] +id: UO:0000010 +name: second +namespace: unit.ontology +def: "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST] +subset: unit_slim +synonym: "s" EXACT [] +is_a: UO:0000003 +is_a: UO:0000045 +created_by: george gkoutos + +[Term] +id: UO:0000012 +name: kelvin +namespace: unit.ontology +def: "A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST] +subset: unit_slim +synonym: "K" EXACT [] +is_a: UO:0000005 +is_a: UO:0000045 +created_by: george gkoutos + +[Term] +id: UO:0000017 +name: micrometer +namespace: unit.ontology +def: "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST] +subset: unit_slim +synonym: "micrometre" EXACT [] +synonym: "micron" EXACT [] +synonym: "um" EXACT [] +is_a: UO:0000001 +created_by: george gkoutos + +[Term] +id: UO:0000018 +name: nanometer +namespace: unit.ontology +def: "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST] +subset: unit_slim +synonym: "nanometre" EXACT [] +synonym: "nm" EXACT [] +is_a: UO:0000001 +created_by: george gkoutos + +[Term] +id: UO:0000021 +name: gram +namespace: unit.ontology +def: "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST] +subset: unit_slim +synonym: "g" EXACT [] +is_a: UO:0000002 +created_by: george gkoutos + +[Term] +id: UO:0000027 +name: degree Celsius +namespace: unit.ontology +def: "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST] +subset: unit_slim +synonym: "C" EXACT [] +is_a: UO:0000005 +created_by: george gkoutos + +[Term] +id: UO:0000028 +name: millisecond +namespace: unit.ontology +def: "A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST] +subset: unit_slim +synonym: "ms" EXACT [] +is_a: UO:0000003 +created_by: george gkoutos + +[Term] +id: UO:0000031 +name: minute +namespace: unit.ontology +def: "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "min" EXACT [] +is_a: UO:0000003 +created_by: george gkoutos + +[Term] +id: UO:0000045 +name: base unit +namespace: unit.ontology +def: "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +created_by: george gkoutos + +[Term] +id: UO:0000047 +name: area unit +namespace: unit.ontology +def: "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001709 +created_by: george gkoutos + +[Term] +id: UO:0000052 +name: mass density unit +namespace: unit.ontology +def: "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG] +subset: unit_group_slim +synonym: "mass per unit volume" EXACT [] +is_a: UO:0000182 +relationship: is_unit_of PATO:0001353 +created_by: george gkoutos + +[Term] +id: UO:0000095 +name: volume unit +namespace: unit.ontology +def: "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001710 +created_by: george gkoutos + +[Term] +id: UO:0000098 +name: milliliter +namespace: unit.ontology +def: "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST] +subset: unit_slim +synonym: "millilitre" EXACT [] +synonym: "ml" EXACT [] +is_a: UO:0000095 +created_by: george gkoutos + +[Term] +id: UO:0000105 +name: frequency unit +namespace: unit.ontology +def: "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0000044 +created_by: george gkoutos + +[Term] +id: UO:0000106 +name: hertz +namespace: unit.ontology +def: "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST] +subset: unit_slim +synonym: "Hz" EXACT [] +synonym: "s^1" EXACT [] +is_a: UO:0000105 +created_by: george gkoutos + +[Term] +id: UO:0000109 +name: pressure unit +namespace: unit.ontology +def: "A unit which is a standard measure of the force applied to a given area." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001025 +created_by: george gkoutos + +[Term] +id: UO:0000110 +name: pascal +namespace: unit.ontology +def: "A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST] +subset: unit_slim +synonym: "Pa" EXACT [] +is_a: UO:0000109 +created_by: george gkoutos + +[Term] +id: UO:0000111 +name: energy unit +namespace: unit.ontology +def: "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001021 +relationship: is_unit_of PATO:0001026 +created_by: george gkoutos + +[Term] +id: UO:0000112 +name: joule +namespace: unit.ontology +def: "An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST] +subset: unit_slim +synonym: "J" EXACT [] +is_a: UO:0000111 +created_by: george gkoutos + +[Term] +id: UO:0000121 +name: angle unit +namespace: unit.ontology +def: "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0000133 +created_by: george gkoutos + +[Term] +id: UO:0000122 +name: plane angle unit +namespace: unit.ontology +def: "A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000121 +created_by: george gkoutos + +[Term] +id: UO:0000150 +name: nanosecond +namespace: unit.ontology +def: "A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST] +subset: unit_slim +synonym: "ns" EXACT [] +is_a: UO:0000003 +created_by: george gkoutos + +[Term] +id: UO:0000166 +name: parts per notation unit +namespace: unit.ontology +def: "A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000186 +created_by: george gkoutos + +[Term] +id: UO:0000169 +name: parts per million +namespace: unit.ontology +def: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG] +subset: unit_slim +synonym: "10^[-6]" EXACT [] +synonym: "ppm" EXACT [] +is_a: UO:0000166 +created_by: george gkoutos + +[Term] +id: UO:0000175 +name: gram per liter +namespace: unit.ontology +def: "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG] +subset: unit_slim +synonym: "g/L" EXACT [] +synonym: "gram per litre" EXACT [] +is_a: UO:0000052 +created_by: george gkoutos + +[Term] +id: UO:0000182 +name: density unit +namespace: unit.ontology +def: "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001019 +created_by: george gkoutos + +[Term] +id: UO:0000185 +name: degree +namespace: unit.ontology +def: "A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia] +subset: unit_slim +is_a: UO:0000122 +created_by: george gkoutos + +[Term] +id: UO:0000186 +name: dimensionless unit +namespace: unit.ontology +def: "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +created_by: george gkoutos + +[Term] +id: UO:0000187 +name: percent +namespace: unit.ontology +def: "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia] +subset: unit_group_slim +synonym: "%" EXACT [] +is_a: UO:0000190 +created_by: george gkoutos + +[Term] +id: UO:0000189 +name: count unit +namespace: unit.ontology +def: "A dimensionless unit which denotes a simple count of things." [MGED:MGED] +subset: unit_group_slim +synonym: "count" EXACT [] +is_a: UO:0000186 +created_by: george gkoutos + +[Term] +id: UO:0000190 +name: ratio +namespace: unit.ontology +def: "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000186 +created_by: george gkoutos + +[Term] +id: UO:0000191 +name: fraction +namespace: unit.ontology +def: "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000190 +created_by: george gkoutos + +[Term] +id: UO:0000217 +name: electric potential difference unit +namespace: unit.ontology +def: "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001464 +created_by: george gkoutos + +[Term] +id: UO:0000218 +name: volt +namespace: unit.ontology +def: "An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "V" EXACT [] +is_a: UO:0000217 +created_by: george gkoutos + +[Term] +id: UO:0000221 +name: dalton +namespace: unit.ontology +def: "An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "amu" EXACT [] +synonym: "Da" EXACT [] +synonym: "u" EXACT [] +synonym: "unified atomic mass unit" EXACT [] +is_a: UO:0000002 +created_by: george gkoutos + +[Term] +id: UO:0000222 +name: kilodalton +namespace: unit.ontology +def: "A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "kDa" EXACT [] +is_a: UO:0000002 +created_by: george gkoutos + +[Term] +id: UO:0000227 +name: magnetic flux density unit +namespace: unit.ontology +def: "A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet] +subset: unit_group_slim +synonym: "B" EXACT [] +is_a: UO:0000000 +created_by: george gkoutos + +[Term] +id: UO:0000228 +name: tesla +namespace: unit.ontology +def: "A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet] +subset: unit_slim +synonym: "T" EXACT [] +synonym: "Wb/m2" EXACT [] +is_a: UO:0000227 +created_by: george gkoutos + +[Term] +id: UO:0000266 +name: electronvolt +namespace: unit.ontology +def: "A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "electron volt" EXACT [] +synonym: "eV" EXACT [] +is_a: UO:0000111 +created_by: george gkoutos + +[Term] +id: UO:0000267 +name: electric field strength unit +namespace: unit.ontology +def: "The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] +subset: unit_group_slim +synonym: "E-field strength " EXACT [] +is_a: UO:0000000 +created_by: george gkoutos +creation_date: 2009-03-03T12:23:16Z + +[Term] +id: UO:0000268 +name: volt per meter +namespace: unit.ontology +def: "The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] +subset: unit_slim +synonym: "V/m" EXACT [] +synonym: "volt per metre" EXACT [] +is_a: UO:0000267 +created_by: george gkoutos +creation_date: 2009-03-03T12:28:17Z + +[Term] +id: UO:0000269 +name: absorbance unit +namespace: unit.ontology +def: "A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\://en.wikipedia.org/wiki/Absorbance] +subset: unit_slim +synonym: "AU" EXACT [] +is_a: UO:0000186 +created_by: george gkoutos +creation_date: 2009-07-14T12:33:48Z + +[Term] +id: UO:0000270 +name: volumetric flow rate unit +namespace: unit.ontology +def: "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +created_by: george gkoutos + +[Term] +id: UO:0000271 +name: microliters per minute +namespace: unit.ontology +def: "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG] +subset: unit_slim +synonym: "microlitres per minute" EXACT [] +synonym: "uL/min" EXACT [] +is_a: UO:0000270 +relationship: is_unit_of PATO:0001574 +created_by: george gkoutos + +[Term] +id: UO:0000324 +name: square angstrom +namespace: unit.ontology +def: "An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long." [UOC:GVG] +synonym: "A^[2]" RELATED [] +is_a: UO:0000047 +created_by: gkoutos +creation_date: 2013-06-27T05:06:40Z + diff --git a/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.owl b/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.owl new file mode 100644 index 00000000..604a5924 --- /dev/null +++ b/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.owl @@ -0,0 +1,75319 @@ + + + + + + + * MS:$sequence(7,0,9999999)$ + * PEFF:$sequence(7,0,9999999)$ + OBO-Edit 2.3.1 + 26:10:2022 11:38 + MS + 1.2 + Joshua Klein + For any queries contact psidev-ms-vocab@lists.sourceforge.net + This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. + To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. + URL: http://purl.obolibrary.org/obo/ms/psi-ms.obo + When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page + coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics + coverage: Mass spectrometer output files and spectra interpretation + creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de> + creator: Chris Bielow <chris.bielow <-at-> fu-berlin.de> + creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org> + creator: Fredrik Levander <fredrik.levander <-at-> immun.lth.se> + creator: Gerhard Mayer <mayerg97 <-at-> rub.de> + creator: Joshua Klein <jaklein <-at-> bu.edu> + creator: Julian Uszkoreit <julian.uszkoreit <-at-> ruhr-uni-bochum.de> + creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de> + creator: Mathias Walzer <walzer <-at-> ebi.ac.uk> + creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu> + creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de> + creator: Pierre-Alain Binz <pierre-alain.binz <-at-> chuv.ch> + creator: Wout Bittremieux <wbittremieux <-at-> health.ucsd.edu> + creator: Yasset Perez-Riverol <yperez <-at-> ebi.ac.uk> + namespace: MS + namespace: PEFF + publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group + + + + + + + + + + + + + definition + + + + + + + + term replaced by + + + + + + + + + + + + + + namespace-id-rule + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_alternative_id + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_format_version + + + + + + + + has_obo_namespace + + + + + + + + has_related_synonym + + + + + + + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MS + has_column + has_column + + + + + + + + MS + has_domain + has_domain + + + + + + + + MS + has_metric_category + has_metric_category + + + + + + + + MS + has_optional_column + has_optional_column + + + + + + + + MS + has_order + has_order + + + + + + + + MS + has_regexp + has regexp + + + + + + + + + + + + + + The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format. + MS + has_structured_representation_in_format + has structured representation in format + + + + + + + + MS + has_units + has_units + + + + + + + + MS + has_value_concept + has_value_concept + + + + + + + + 'Entity A' has value type 'Entity B', such as xsd:float. + MS + has_value_type + has value type + + + + + + + + + + + + + + + MS + part_of + part_of + + + + + + + + + + + + + Proteomics Standards Initiative Mass Spectrometry Vocabularies. + MS + MS:0000000 + Proteomics Standards Initiative Mass Spectrometry Vocabularies + + + + + Proteomics Standards Initiative Mass Spectrometry Vocabularies. + PSI:MS + + + + + + + + + + + + + + + A reference number relevant to the sample under study. + MS + MS:1000001 + sample number + + + + + A reference number relevant to the sample under study. + PSI:MS + + + + + + + + + + + + + + + A reference string relevant to the sample under study. + MS + MS:1000002 + sample name + + + + + A reference string relevant to the sample under study. + PSI:MS + + + + + + + + + The chemical phase of a pure sample, or the state of a mixed sample. + MS + MS:1000003 + sample state + + + + + The chemical phase of a pure sample, or the state of a mixed sample. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Total mass of sample used. + MS + MS:1000004 + sample mass + + + + + Total mass of sample used. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Total volume of solution used. + MS + MS:1000005 + sample volume + + + + + Total volume of solution used. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used. + MS + MS:1000006 + sample concentration + + + + + Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used. + PSI:MS + + + + + + + + + + + + + + The nature of the sample inlet. + MS + MS:1000007 + inlet type + + + + + The nature of the sample inlet. + PSI:MS + + + + + + + + + + + + + + The method by which gas phase ions are generated from the sample. + MS + MS:1000008 + ionization type + + + + + The method by which gas phase ions are generated from the sample. + PSI:MS + + + + + + + + OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer. + MS + MS:1000009 + This term was made obsolete because it was replaced by scan polarity (MS:1000465). + ionization mode + true + + + + + OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer. + PSI:MS + + + + + + + + OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted. + MS + MS:1000010 + This former purgatory term was made obsolete. + analyzer type + true + + + + + OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted. + PSI:MS + + + + + + + + + + + + + + + Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height. + MS + MS:1000011 + mass resolution + + + + + Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height. + PSI:MS + + + + + + + + + Which of the available standard measures is used to define whether two peaks are separate. + MS + MS:1000012 + resolution measurement method + + + + + Which of the available standard measures is used to define whether two peaks are separate. + PSI:MS + + + + + + + + OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z. + MS + MS:1000013 + This former purgatory term was made obsolete. + resolution type + true + + + + + OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + Accuracy is the degree of conformity of a measured mass to its actual value. + MS + MS:1000014 + accuracy + + + + + Accuracy is the degree of conformity of a measured mass to its actual value. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Rate in Th/sec for scanning analyzers. + MS + MS:1000015 + scan rate + + + + + Rate in Th/sec for scanning analyzers. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + The time that an analyzer started a scan, relative to the start of the MS run. + MS + MS:1000016 + scan start time + + + + + The time that an analyzer started a scan, relative to the start of the MS run. + PSI:MS + + + + + + + + OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum. + MS + MS:1000017 + OBSOLETE This former purgatory term was made obsolete. + Scan Function + true + + + + + OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum. + PSI:MS + + + + + + + + + + + + + + Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low). + MS + MS:1000018 + scan direction + + + + + Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low). + PSI:MS + + + + + + + + + + + + + + Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used. + MS + MS:1000019 + scan law + + + + + Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used. + PSI:MS + + + + + + + + Describes the acquisition data type produced by a tandem mass spectrometry experiment. + MS + Tandem Scanning Method + MS:1000020 + OBSOLETE This former purgatory term was made obsolete. + scanning method + true + + + + + Describes the acquisition data type produced by a tandem mass spectrometry experiment. + PSI:MS + + + + + + + + + Status of the reflectron, turned on or off. + MS + MS:1000021 + reflectron state + + + + + Status of the reflectron, turned on or off. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The length of the field free drift space in a time of flight mass spectrometer. + MS + MS:1000022 + TOF Total Path Length + + + + + The length of the field free drift space in a time of flight mass spectrometer. + PSI:MS + + + + + + + + + + + + + + + + + + + + OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion. + MS + MS:1000023 + This former purgatory term was made obsolete. + isolation width + true + + + + + OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion. + PSI:MS + + + + + + + + + + + + + + + Final MS level achieved when performing PFF with the ion trap (e.g. MS E10). + MS + MS:1000024 + final MS exponent + + + + + Final MS level achieved when performing PFF with the ion trap (e.g. MS E10). + PSI:MS + + + + + + + + + + + + + + + + + + + + + A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity. + B + MS + Magnetic Field + MS:1000025 + magnetic field strength + + + + + A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity. + PSI:MS + + + + + + + + + + + + + + Type of detector used in the mass spectrometer. + MS + MS:1000026 + detector type + + + + + Type of detector used in the mass spectrometer. + PSI:MS + + + + + + + + + + + + + + Method by which detector signal is acquired by the data system. + MS + MS:1000027 + detector acquisition mode + + + + + Method by which detector signal is acquired by the data system. + PSI:MS + + + + + + + + + + + + + + + The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height. + MS + MS:1000028 + detector resolution + + + + + The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The rate of signal sampling (measurement) with respect to time. + ADC Sampling Frequency + MS + MS:1000029 + sampling frequency + + + + + The rate of signal sampling (measurement) with respect to time. + PSI:MS + + + + + + + + OBSOLETE Name of instrument vendor. + MS + MS:1000030 + This term was made obsolete because it was replaced by instrument model (MS:1000031). + vendor + true + + + + + OBSOLETE Name of instrument vendor. + PSI:MS + + + + + + + + + + + + + + Instrument model name not including the vendor's name. + MS + MS:1000031 + instrument model + + + + + Instrument model name not including the vendor's name. + PSI:MS + + + + + + + + + + + + + + + Free text description of a single customization made to the instrument; for several modifications, use several entries. + MS + MS:1000032 + customization + + + + + Free text description of a single customization made to the instrument; for several modifications, use several entries. + PSI:MS + + + + + + + + + The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution. + MS + MS:1000033 + deisotoping + + + + + The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution. + PSI:MS + + + + + + + + + The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions. + MS + MS:1000034 + charge deconvolution + + + + + The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions. + PSI:MS + + + + + + + + + Spectral peak processing conducted on the acquired data to convert profile data to centroided data. + MS + MS:1000035 + peak picking + + + + + Spectral peak processing conducted on the acquired data to convert profile data to centroided data. + PSI:MS + + + + + + + + OBSOLETE. + MS + MS:1000036 + This term was made obsolete because . + scan mode + true + + + + + OBSOLETE. + PSI:MS + + + + + + + + OBSOLETE Terms to describe the polarity setting of the instrument. + MS + MS:1000037 + This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186). + polarity + true + + + + + OBSOLETE Terms to describe the polarity setting of the instrument. + PSI:MS + + + + + + + + OBSOLETE Acquisition time in minutes. + MS + MS:1000038 + This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031). + minute + true + + + + + OBSOLETE Acquisition time in minutes. + PSI:MS + + + + + + + + OBSOLETE Acquisition time in seconds. + MS + MS:1000039 + This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010). + second + true + + + + + OBSOLETE Acquisition time in seconds. + PSI:MS + + + + + + + + + Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated. + Th + mass-to-charge ratio + thomson + MS + MS:1000040 + m/z + + + + + Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated. + PSI:MS + + + + + + + + + + + + + + + + Number of net charges, positive or negative, on an ion. + z + MS + MS:1000041 + charge state + + + + + Number of net charges, positive or negative, on an ion. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Intensity of ions as measured by the height or area of a peak in a mass spectrum. + MS + MS:1000042 + peak intensity + + + + + Intensity of ions as measured by the height or area of a peak in a mass spectrum. + PSI:MS + + + + + + + + + Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors. + MS + MS:1000043 + intensity unit + + + + + Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors. + PSI:MS + + + + + + + + + + + + + + Fragmentation method used for dissociation or fragmentation. + MS + Activation Method + MS:1000044 + dissociation method + + + + + Fragmentation method used for dissociation or fragmentation. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. + MS + MS:1000045 + collision energy + + + + + Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. + PSI:MS + + + + + + + + + OBSOLETE Energy units are represented in either eV or Joules. + MS + MS:1000046 + This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111). + energy unit + true + + + + + OBSOLETE Energy units are represented in either eV or Joules. + PSI:MS + + + + + + + + + State if the sample is in emulsion form. + MS + MS:1000047 + emulsion + + + + + State if the sample is in emulsion form. + PSI:MS + + + + + + + + + State if the sample is in gaseous form. + MS + MS:1000048 + gaseous sample state + + + + + State if the sample is in gaseous form. + PSI:MS + + + + + + + + + State if the sample is in liquid form. + MS + MS:1000049 + liquid sample state + + + + + State if the sample is in liquid form. + PSI:MS + + + + + + + + + State if the sample is in solid form. + MS + MS:1000050 + solid sample state + + + + + State if the sample is in solid form. + PSI:MS + + + + + + + + + State if the sample is in solution form. + MS + MS:1000051 + solution + + + + + State if the sample is in solution form. + PSI:MS + + + + + + + + + State if the sample is in suspension form. + MS + MS:1000052 + suspension + + + + + State if the sample is in suspension form. + PSI:MS + + + + + + + + + + + + + + + Sample batch lot identifier. + MS + MS:1000053 + sample batch + + + + + Sample batch lot identifier. + PSI:MS + + + + + + + + OBSOLETE Chromatographic conditions used to obtain the sample. + MS + MS:1000054 + This former purgatory term was made obsolete. + chromatography + true + + + + + OBSOLETE Chromatographic conditions used to obtain the sample. + PSI:MS + + + + + + + + + Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix. + CF-FAB + MS + MS:1000055 + continuous flow fast atom bombardment + + + + + Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix. + PSI:MS + + + + + + + + + The sample is directly inserted into the ion source, usually on the end of a heatable probe. + MS + MS:1000056 + direct inlet + + + + + The sample is directly inserted into the ion source, usually on the end of a heatable probe. + PSI:MS + + + + + + + + + Inlet used for introducing the liquid sample into an electrospray ionization source. + MS + MS:1000057 + electrospray inlet + + + + + Inlet used for introducing the liquid sample into an electrospray ionization source. + PSI:MS + + + + + + + + + Sample is directly injected or infused into the ionization source. + MS + MS:1000058 + flow injection analysis + + + + + Sample is directly injected or infused into the ionization source. + PSI:MS + + + + + + + + + A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction. + MS + MS:1000059 + inductively coupled plasma + + + + + A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction. + PSI:MS + + + + + + + + + The continuous flow of solution of a sample into the ionization source. + MS + MS:1000060 + infusion + + + + + The continuous flow of solution of a sample into the ionization source. + PSI:MS + + + + + + + + + A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity. + MS + MS:1000061 + jet separator + + + + + A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity. + PSI:MS + + + + + + + + + A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane. + MS + MS:1000062 + membrane separator + + + + + A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane. + PSI:MS + + + + + + + + + Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules. + MS + MS:1000063 + moving belt + + + + + Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules. + PSI:MS + + + + + + + + + Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules. + MS + MS:1000064 + moving wire + + + + + Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules. + PSI:MS + + + + + + + + + A division of flowing stream of liquid into two streams. + MS + MS:1000065 + open split + + + + + A division of flowing stream of liquid into two streams. + PSI:MS + + + + + + + + + Method for generating ions from a solution of an analyte. + MS + MS:1000066 + particle beam + + + + + Method for generating ions from a solution of an analyte. + PSI:MS + + + + + + + + + A sample inlet method involving a reservoir. + MS + MS:1000067 + reservoir + + + + + A sample inlet method involving a reservoir. + PSI:MS + + + + + + + + + A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber. + MS + MS:1000068 + septum + + + + + A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber. + PSI:MS + + + + + + + + + A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample. + MS + MS:1000069 + thermospray inlet + + + + + A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample. + PSI:MS + + + + + + + + + Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization. + APCI + MS + MS:1000070 + atmospheric pressure chemical ionization + + + + + Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization. + PSI:MS + + + + + + + + + The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization. + CI + MS + MS:1000071 + chemical ionization + + + + + The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization. + PSI:MS + + + + + + + + OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. + EI + MS + MS:1000072 + This term was made obsolete because it was replaced by electron ionization (MS:1000389). + Electronic Ionization + true + + + + + OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. + PSI:MS + + + + + + + + + A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended. + ESI + MS + MS:1000073 + electrospray ionization + + + + + A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended. + PSI:MS + + + + + + + + + The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization. + FAB + MS + MS:1000074 + fast atom bombardment ionization + + + + + The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization. + PSI:MS + + + + + + + + + The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization. + MALDI + MS + MS:1000075 + matrix-assisted laser desorption ionization + + + + + The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization. + PSI:MS + + + + + + + + OBSOLETE. + MS + MS:1000076 + This term was made obsolete because it was replaced by negative scan (MS:1000129). + negative ion mode + true + + + + + OBSOLETE. + PSI:MS + + + + + + + + OBSOLETE. + MS + MS:1000077 + This term was made obsolete because it was replaced by positive scan (MS:1000130). + positive ion mode + true + + + + + OBSOLETE. + PSI:MS + + + + + + + + + A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer. + MS + MS:1000078 + axial ejection linear ion trap + + + + + A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer. + PSI:MS + + + + + + + + + A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z. + FT_ICR + MS + MS:1000079 + fourier transform ion cyclotron resonance mass spectrometer + + + + + A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z. + PSI:MS + + + + + + + + + A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z. + MS + MS:1000080 + magnetic sector + + + + + A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z. + PSI:MS + + + + + + + + + A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. + MS + MS:1000081 + quadrupole + + + + + A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. + PSI:MS + + + + + + + + + Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials. + Paul Ion trap + QIT + Quistor + MS + MS:1000082 + quadrupole ion trap + + + + + Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials. + PSI:MS + + + + + + + + + A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer. + MS + MS:1000083 + radial ejection linear ion trap + + + + + A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer. + PSI:MS + + + + + + + + + Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy. + TOF + MS + MS:1000084 + time-of-flight + + + + + Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy. + PSI:MS + + + + + + + + + An attribute of resolution when recording the detector response in absence of the analyte. + MS + MS:1000085 + baseline + + + + + An attribute of resolution when recording the detector response in absence of the analyte. + PSI:MS + + + + + + + + + A measure of resolution represented as width of the peak at half peak height. + FWHM + MS + MS:1000086 + full width at half-maximum + + + + + A measure of resolution represented as width of the peak at half peak height. + PSI:MS + + + + + + + + + An attribute of resolution when the ratio between adjacent signals is 10% of the signal height. + MS + MS:1000087 + ten percent valley + + + + + An attribute of resolution when the ratio between adjacent signals is 10% of the signal height. + PSI:MS + + + + + + + + OBSOLETE When resolution is constant with respect to m/z. + MS + MS:1000088 + This child of the former purgatory term resolution type was made obsolete. + constant + true + + + + + OBSOLETE When resolution is constant with respect to m/z. + PSI:MS + + + + + + + + OBSOLETE When resolution is proportional with respect to m/z. + MS + MS:1000089 + This child of the former purgatory term resolution type was made obsolete. + proportional + true + + + + + OBSOLETE When resolution is proportional with respect to m/z. + PSI:MS + + + + + + + + OBSOLETE A variation of instrument where a selected mass is scanned. + MS + MS:1000090 + This child of the former purgatory term Scan Function was made obsolete. + mass scan + true + + + + + OBSOLETE A variation of instrument where a selected mass is scanned. + PSI:MS + + + + + + + + OBSOLETE Please see Single Ion Monitoring. + MS + MS:1000091 + This child of the former purgatory term Scan Function was made obsolete. + selected ion detection + true + + + + + OBSOLETE Please see Single Ion Monitoring. + PSI:MS + + + + + + + + + High to low direction in terms of m/z of the scan for scanning analyzers. + MS + MS:1000092 + decreasing m/z scan + + + + + High to low direction in terms of m/z of the scan for scanning analyzers. + PSI:MS + + + + + + + + + Low to high direction in terms of m/z of the scan for scanning analyzers. + MS + MS:1000093 + increasing m/z scan + + + + + Low to high direction in terms of m/z of the scan for scanning analyzers. + PSI:MS + + + + + + + + + The mass scan is done in exponential mode. + MS + MS:1000094 + exponential + + + + + The mass scan is done in exponential mode. + PSI:MS + + + + + + + + + OBSOLETE The mass scan is done in linear mode. + MS + MS:1000095 + This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199). + linear + true + + + + + OBSOLETE The mass scan is done in linear mode. + PSI:MS + + + + + + + + + The mass scan is done in quadratic mode. + MS + MS:1000096 + quadratic + + + + + The mass scan is done in quadratic mode. + PSI:MS + + + + + + + + OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. + MS + MS:1000097 + This former purgatory term was made obsolete. + constant neutral mass loss + true + + + + + OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. + PSI:MS + + + + + + + + OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring. + MS + MS:1000098 + This former purgatory term was made obsolete. + multiple ion monitoring + true + + + + + OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring. + PSI:MS + + + + + + + + OBSOLETE This term is not recommended. See Selected Reaction Monitoring. + MRM + MS + MS:1000099 + This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206). + multiple reaction monitoring + true + + + + + OBSOLETE This term is not recommended. See Selected Reaction Monitoring. + PSI:MS + + + + + + + + OBSOLETE The specific scan function or process that will record a precursor ion spectrum. + MS + MS:1000100 + This former purgatory term was made obsolete. + precursor ion scan + true + + + + + OBSOLETE The specific scan function or process that will record a precursor ion spectrum. + PSI:MS + + + + + + + + OBSOLETE The specific scan function or process that records product ion spectrum. + MS + MS:1000101 + This former purgatory term was made obsolete. + product ion scan + true + + + + + OBSOLETE The specific scan function or process that records product ion spectrum. + PSI:MS + + + + + + + + OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum. + MS + MS:1000102 + This term was made obsolete because it was replaced by single ion monitoring (MS:100205). + single ion monitoring + true + + + + + OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum. + PSI:MS + + + + + + + + OBSOLETE This term is not recommended. See Selected Reaction Monitoring. + MS + MS:1000103 + This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206). + single reaction monitoring + true + + + + + OBSOLETE This term is not recommended. See Selected Reaction Monitoring. + PSI:MS + + + + + + + + OBSOLETE None. + MS + MS:1000104 + This term was made obsolete because . + None ?? + true + + + + + OBSOLETE None. + PSI:MS + + + + + + + + + Reflectron is off. + MS + MS:1000105 + reflectron off + + + + + Reflectron is off. + PSI:MS + + + + + + + + + Reflectron is on. + MS + MS:1000106 + reflectron on + + + + + Reflectron is on. + PSI:MS + + + + + + + + + A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse. + Channeltron Detector + MS + MS:1000107 + channeltron + + + + + A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse. + PSI:MS + + + + + + + + + A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected. + MS + MS:1000108 + conversion dynode electron multiplier + + + + + A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected. + PSI:MS + + + + + + + + + A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier. + MS + ion-to-photon detector + MS:1000109 + conversion dynode photomultiplier + + + + + A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier. + PSI:MS + + + + + + + + + Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector. + Daly + MS + MS:1000110 + daly detector + + + + + Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector. + PSI:MS + + + + + + + + + A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. + EMT + MS + MS:1000111 + electron multiplier tube + + + + + A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. + PSI:MS + + + + + + + + + A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device. + MS + MS:1000112 + faraday cup + + + + + A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device. + PSI:MS + + + + + + + + + An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. + MS + MS:1000113 + focal plane array + + + + + An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. + PSI:MS + + + + + + + + + A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate. + multichannel plate + MS + MS:1000114 + microchannel plate detector + + + + + A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate. + PSI:MS + + + + + + + + + A detector system commonly used in inductively coupled plasma mass spectrometers. + MS + MS:1000115 + multi-collector + + + + + A detector system commonly used in inductively coupled plasma mass spectrometers. + PSI:MS + + + + + + + + + A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected. + PMT + MS + MS:1000116 + photomultiplier + + + + + A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected. + PSI:MS + + + + + + + + + Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers. + ADC + MS + MS:1000117 + analog-digital converter + + + + + Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers. + PSI:MS + + + + + + + + + Definition to do. + MS + MS:1000118 + pulse counting + + + + + Definition to do. + PSI:MS + + + + + + + + + A device for converting a signal of sporadic pluses into a digital representation of their time indices. + TDC + MS + MS:1000119 + time-digital converter + + + + + A device for converting a signal of sporadic pluses into a digital representation of their time indices. + PSI:MS + + + + + + + + + A detector acquisition mode used for detecting transient signals. + MS + MS:1000120 + transient recorder + + + + + A detector acquisition mode used for detecting transient signals. + PSI:MS + + + + + + + + + The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as "Applied Biosystems|MDS SCIEX". + MS + Applied Biosystems|MDS SCIEX + MS:1000121 + SCIEX instrument model + + + + + The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as "Applied Biosystems|MDS SCIEX". + PSI:MS + + + + + + + + + Bruker Daltonics' instrument model. + MS + MS:1000122 + Bruker Daltonics instrument model + + + + + Bruker Daltonics' instrument model. + PSI:MS + + + + + + + + + IonSpec corporation instrument model. + MS + MS:1000123 + IonSpec instrument model + + + + + IonSpec corporation instrument model. + PSI:MS + + + + + + + + + Shimadzu corporation instrument model. + MS + MS:1000124 + Shimadzu instrument model + + + + + Shimadzu corporation instrument model. + PSI:MS + + + + + + + + + ThermoFinnigan from Thermo Electron Corporation instrument model. + MS + MS:1000125 + Thermo Finnigan instrument model + + + + + ThermoFinnigan from Thermo Electron Corporation instrument model. + PSI:MS + + + + + + + + + Waters Corporation instrument model. + MS + MS:1000126 + Waters instrument model + + + + + Waters Corporation instrument model. + PSI:MS + + + + + + + + + Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. + Discrete Mass Spectrum + MS + MS:1000127 + centroid spectrum + + + + + Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset. + PSI:MS + + + + + + + + + A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. + Continuum Mass Spectrum + continuous mass spectrum + MS + MS:1000128 + profile spectrum + + + + + A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis. + PSI:MS + + + + + + + + + + Polarity of the scan is negative. + MS + MS:1000129 + negative scan + + + + + Polarity of the scan is negative. + PSI:MS + + + + + + + + + + Polarity of the scan is positive. + MS + MS:1000130 + positive scan + + + + + Polarity of the scan is positive. + PSI:MS + + + + + + + + + The number of counted events observed in one or a group of elements of a detector. + MS + MS:1000131 + number of detector counts + + + + + The number of counted events observed in one or a group of elements of a detector. + PSI:MS + + + + + + + + + + + + + + + The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity. + MS + MS:1000132 + percent of base peak + + + + + The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity. + PSI:MS + + + + + + + + + The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended. + CAD + CID + collisionally activated dissociation + MS + MS:1000133 + collision-induced dissociation + + + + + The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended. + PSI:MS + + + + + + + + + The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. + PD + MS + MS:1000134 + plasma desorption + + + + + The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. + PSI:MS + + + + + + + + + A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra. + PSD + MS + MS:1000135 + post-source decay + + + + + A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra. + PSI:MS + + + + + + + + + Fragmentation that results from the collision of an ion with a surface. + SID + MS + MS:1000136 + surface-induced dissociation + + + + + Fragmentation that results from the collision of an ion with a surface. + PSI:MS + + + + + + + + OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J. + MS + MS:1000137 + This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266). + electron volt + true + + + + + OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions. + MS + MS:1000138 + normalized collision energy + + + + + Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions. + PSI:PI + + + + + + + + + Applied Biosystems/MDS SCIEX Q 4000 TRAP MS. + MS + MS:1000139 + 4000 QTRAP + + + + + Applied Biosystems/MDS SCIEX Q 4000 TRAP MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS. + MS + MS:1000140 + 4700 Proteomics Analyzer + + + + + Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS. + PSI:MS + + + + + + + + + Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. + MS + MS:1000141 + apex IV + + + + + Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. + PSI:MS + + + + + + + + + Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. + MS + MS:1000142 + apex Q + + + + + Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 150EX MS. + MS + MS:1000143 + API 150EX + + + + + Applied Biosystems/MDS SCIEX API 150EX MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 150EX Prep MS. + MS + MS:1000144 + API 150EX Prep + + + + + Applied Biosystems/MDS SCIEX API 150EX Prep MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 2000 MS. + MS + MS:1000145 + API 2000 + + + + + Applied Biosystems/MDS SCIEX API 2000 MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 3000 MS. + MS + MS:1000146 + API 3000 + + + + + Applied Biosystems/MDS SCIEX API 3000 MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 4000 MS. + MS + MS:1000147 + API 4000 + + + + + Applied Biosystems/MDS SCIEX API 4000 MS. + PSI:MS + + + + + + + + + Bruker Daltonics' autoflex II: MALDI TOF. + MS + MS:1000148 + autoflex II + + + + + Bruker Daltonics' autoflex II: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF. + MS + MS:1000149 + autoflex TOF/TOF + + + + + Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF. + PSI:MS + + + + + + + + + Waters magnetic sector based AutoSpec Ultima NT MS. + MS + MS:1000150 + Auto Spec Ultima NT + + + + + Waters magnetic sector based AutoSpec Ultima NT MS. + PSI:MS + + + + + + + + + Bruker Daltonics' BioTOF II: ESI TOF. + MS + MS:1000151 + BioTOF II + + + + + Bruker Daltonics' BioTOF II: ESI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' BioTOF-Q: ESI Q-TOF. + MS + MS:1000152 + BioTOF-Q + + + + + Bruker Daltonics' BioTOF-Q: ESI Q-TOF. + PSI:MS + + + + + + + + + ThermoFinnigan DELTA plusAdvantage MS. + MS + MS:1000153 + DELTA plusAdvantage + + + + + ThermoFinnigan DELTA plusAdvantage MS. + PSI:MS + + + + + + + + + ThermoFinnigan DELTAplusXP MS. + MS + MS:1000154 + DELTAplusXP + + + + + ThermoFinnigan DELTAplusXP MS. + PSI:MS + + + + + + + + OBSOLETE ThermoFinnigan ELEMENT2 MS. + MS + MS:1000155 + This former purgatory term was made obsolete. + ELEMENT2 + true + + + + + OBSOLETE ThermoFinnigan ELEMENT2 MS. + PSI:MS + + + + + + + + + Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. + MS + MS:1000156 + esquire 4000 + + + + + Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. + MS + MS:1000157 + esquire 6000 + + + + + Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + IonSpec Explorer MS. + MS + MS:1000158 + explorer + + + + + IonSpec Explorer MS. + PSI:MS + + + + + + + + + Waters oa-ToF based GCT. + MS + MS:1000159 + GCT + + + + + Waters oa-ToF based GCT. + PSI:MS + + + + + + + + + Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI. + MS + MS:1000160 + HCT + + + + + Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI. + MS + MS:1000161 + HCTplus + + + + + Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + IonSpec HiResESI MS. + MS + MS:1000162 + HiRes ESI + + + + + IonSpec HiResESI MS. + PSI:MS + + + + + + + + + IonSpec HiResMALDI MS. + MS + MS:1000163 + HiRes MALDI + + + + + IonSpec HiResMALDI MS. + PSI:MS + + + + + + + + + Waters IsoPrime MS. + MS + MS:1000164 + IsoPrime + + + + + Waters IsoPrime MS. + PSI:MS + + + + + + + + + Waters IsoProbe MS. + MS + MS:1000165 + IsoProbe + + + + + Waters IsoProbe MS. + PSI:MS + + + + + + + + + Waters IsoProbe T MS. + MS + MS:1000166 + IsoProbe T + + + + + Waters IsoProbe T MS. + PSI:MS + + + + + + + + + ThermoFinnigan LCQ Advantage MS. + MS + MS:1000167 + LCQ Advantage + + + + + ThermoFinnigan LCQ Advantage MS. + PSI:MS + + + + + + + + + ThermoFinnigan LCQ Classic MS. + MS + MS:1000168 + LCQ Classic + + + + + ThermoFinnigan LCQ Classic MS. + PSI:MS + + + + + + + + + ThermoFinnigan LCQ Deca XP Plus MS. + MS + MS:1000169 + LCQ Deca XP Plus + + + + + ThermoFinnigan LCQ Deca XP Plus MS. + PSI:MS + + + + + + + + + Waters oa-ToF based MALDI L. + MS + MS:1000170 + M@LDI L + + + + + Waters oa-ToF based MALDI L. + PSI:MS + + + + + + + + + Waters oa-ToF based MALDI LR. + MS + MS:1000171 + M@LDI LR + + + + + Waters oa-ToF based MALDI LR. + PSI:MS + + + + + + + + + ThermoFinnigan MAT253 MS. + MS + MS:1000172 + MAT253 + + + + + ThermoFinnigan MAT253 MS. + PSI:MS + + + + + + + + + ThermoFinnigan MAT900XP MS. + MS + MS:1000173 + MAT900XP + + + + + ThermoFinnigan MAT900XP MS. + PSI:MS + + + + + + + + + ThermoFinnigan MAT900XP Trap MS. + MS + MS:1000174 + MAT900XP Trap + + + + + ThermoFinnigan MAT900XP Trap MS. + PSI:MS + + + + + + + + + ThermoFinnigan MAT95XP MS. + MS + MS:1000175 + MAT95XP + + + + + ThermoFinnigan MAT95XP MS. + PSI:MS + + + + + + + + + ThermoFinnigan MAT95XP Trap MS. + MS + MS:1000176 + MAT95XP Trap + + + + + ThermoFinnigan MAT95XP Trap MS. + PSI:MS + + + + + + + + + Bruker Daltonics' microflex: MALDI TOF. + MS + MS:1000177 + microflex + + + + + Bruker Daltonics' microflex: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI. + MS + MS:1000178 + microTOF LC + + + + + Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + ThermoFinnigan NEPTUNE MS. + MS + MS:1000179 + neptune + + + + + ThermoFinnigan NEPTUNE MS. + PSI:MS + + + + + + + + + Waters NG-5400 MS. + MS + MS:1000180 + NG-5400 + + + + + Waters NG-5400 MS. + PSI:MS + + + + + + + + + IonSpec OMEGA MS. + MS + MS:1000181 + OMEGA + + + + + IonSpec OMEGA MS. + PSI:MS + + + + + + + + + IonSpec OMEGA-2001 MS. + MS + MS:1000182 + OMEGA-2001 + + + + + IonSpec OMEGA-2001 MS. + PSI:MS + + + + + + + + + Bruker Daltonics' OmniFlex: MALDI TOF. + MS + MS:1000183 + OmniFlex + + + + + Bruker Daltonics' OmniFlex: MALDI TOF. + PSI:MS + + + + + + + + + Waters Platform ICP MS. + MS + MS:1000184 + Platform ICP + + + + + Waters Platform ICP MS. + PSI:MS + + + + + + + + + ThermoFinnigan PolarisQ MS. + MS + MS:1000185 + PolarisQ + + + + + ThermoFinnigan PolarisQ MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS. + MS + MS:1000186 + proteomics solution 1 + + + + + Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX Q TRAP MS. + MS + MS:1000187 + Q TRAP + + + + + Applied Biosystems/MDS SCIEX Q TRAP MS. + PSI:MS + + + + + + + + + Waters oa-ToF based Q-Tof micro. + MS + MS:1000188 + Q-Tof micro + + + + + Waters oa-ToF based Q-Tof micro. + PSI:MS + + + + + + + + + Waters oa-ToF based Q-Tof Ultima. + MS + MS:1000189 + Q-Tof Ultima + + + + + Waters oa-ToF based Q-Tof Ultima. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX QSTAR MS. + MS + MS:1000190 + QSTAR + + + + + Applied Biosystems/MDS SCIEX QSTAR MS. + PSI:MS + + + + + + + + + Waters (triple) quadrupole based micro. + MS + MS:1000191 + quattro micro + + + + + Waters (triple) quadrupole based micro. + PSI:MS + + + + + + + + + Waters (triple) quadrupole based Ultima. + MS + MS:1000192 + Quattro Ultima + + + + + Waters (triple) quadrupole based Ultima. + PSI:MS + + + + + + + + + ThermoFinnigan Surveyor MSQ MS. + MS + MS:1000193 + Surveyor MSQ + + + + + ThermoFinnigan Surveyor MSQ MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX SymBiot I MS. + MS + MS:1000194 + SymBiot I + + + + + Applied Biosystems/MDS SCIEX SymBiot I MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX SymBiot XVI MS. + MS + MS:1000195 + SymBiot XVI + + + + + Applied Biosystems/MDS SCIEX SymBiot XVI MS. + PSI:MS + + + + + + + + + ThermoFinnigan TEMPUS TOF MS. + MS + MS:1000196 + TEMPUS TOF + + + + + ThermoFinnigan TEMPUS TOF MS. + PSI:MS + + + + + + + + + ThermoFinnigan TRACE DSQ MS. + MS + MS:1000197 + TRACE DSQ + + + + + ThermoFinnigan TRACE DSQ MS. + PSI:MS + + + + + + + + + ThermoFinnigan TRITON MS. + MS + MS:1000198 + TRITON + + + + + ThermoFinnigan TRITON MS. + PSI:MS + + + + + + + + + ThermoFinnigan TSQ Quantum MS. + MS + MS:1000199 + TSQ Quantum + + + + + ThermoFinnigan TSQ Quantum MS. + PSI:MS + + + + + + + + + IonSpec Ultima MS. + MS + MS:1000200 + ultima + + + + + IonSpec Ultima MS. + PSI:MS + + + + + + + + + Bruker Daltonics' ultraflex: MALDI TOF. + MS + MS:1000201 + ultraflex + + + + + Bruker Daltonics' ultraflex: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF. + MS + MS:1000202 + ultraflex TOF/TOF + + + + + Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX Voyager-DE PRO MS. + MS + MS:1000203 + Voyager-DE PRO + + + + + Applied Biosystems/MDS SCIEX Voyager-DE PRO MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX Voyager-DE STR MS. + MS + MS:1000204 + Voyager-DE STR + + + + + Applied Biosystems/MDS SCIEX Voyager-DE STR MS. + PSI:MS + + + + + + + + + + The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum. + Multiple Ion Monitoring + SIM + MS + MIM + MS:1000205 + selected ion monitoring + + + + + The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum. + PSI:MS + + + + + + + + + + Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space. + SRM + MS + MRM + Multiple Reaction Monitoring + MS:1000206 + selected reaction monitoring + + + + + Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space. + PSI:MS + + + + + + + + + + + + + + + + + + + + OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition. + MS + MS:1000207 + This child of the former purgatory term ion attribute was made obsolete. + accurate mass + true + + + + + OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition. + PSI:MS + + + + + + + + + + + + + + + + + + + + OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance. + MS + MS:1000208 + This child of the former purgatory term ion attribute was made obsolete. + average mass + true + + + + + OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance. + PSI:MS + + + + + + + + + + + + + + + + + + + + OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended. + AE + MS + MS:1000209 + This child of the former purgatory term ion attribute was made obsolete. + appearance energy + true + + + + + OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended. + PSI:MS + + + + + + + + + The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures. + BP + MS + MS:1000210 + base peak + + + + + The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures. + PSI:MS + + + + + + + + + + + + + + OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state. + MS + MS:1000211 + OBSOLETE charge number + true + + + + + OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state. + PSI:MS + + + + + + + + OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg. + MS + MS:1000212 + This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221). + dalton + true + + + + + OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg. + PSI:MS + + + + + + + + + + + + + + OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy. + EA + MS + MS:1000213 + This child of the former purgatory term ion attribute was made obsolete. + electron affinity + true + + + + + OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy. + PSI:MS + + + + + + + + OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization. + MS + MS:1000214 + This former purgatory term was made obsolete. + electron energy obsolete + true + + + + + OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization. + PSI:MS + + + + + + + + + + + + + + + + + + + + OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom. + MS + MS:1000215 + This child of the former purgatory term ion attribute was made obsolete. + exact mass + true + + + + + OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom. + PSI:MS + + + + + + + + + A section of a mass spectrometer in which there are no electric or magnetic fields. + FFR + MS + MS:1000216 + field-free region + + + + + A section of a mass spectrometer in which there are no electric or magnetic fields. + PSI:MS + + + + + + + + OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule. + MS + MS:1000217 + This child of the former purgatory term ion reaction was made obsolete. + ionization cross section + true + + + + + OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule. + PSI:MS + + + + + + + + + + + + + + OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used. + MS + MS:1000218 + This term was made obsolete because it was replaced by ionization efficiency (MS:1000392). + ionization efficiency + true + + + + + OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used. + PSI:MS + + + + + + + + + + + + + + + + + + + + OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion. + IE + MS + MS:1000219 + This child of the former purgatory term ion attribute was made obsolete. + ionization energy + true + + + + + OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion. + PSI:MS + + + + + + + + OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard. + IDMS + MS + MS:1000220 + This child of the former purgatory term mass spectrometry was made obsolete. + isotope dilution mass spectrometry + true + + + + + OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard. + PSI:MS + + + + + + + + + The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer. + MS + MS:1000221 + magnetic deflection + + + + + The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer. + PSI:MS + + + + + + + + + + + + + + + + + + + + OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom. + MS + MS:1000222 + This child of the former purgatory term ion attribute was made obsolete. + mass defect + true + + + + + OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom. + PSI:MS + + + + + + + + + + + + + + OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion. + MS + MS:1000223 + This child of the former purgatory term ion attribute was made obsolete. + mass number + true + + + + + OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Mass of a molecule measured in unified atomic mass units (u or Da). + MS + MS:1000224 + molecular mass + + + + + Mass of a molecule measured in unified atomic mass units (u or Da). + https://en.wikipedia.org/wiki/Molecular_mass + + + + + + + + + + + + + + + + + + + + OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element. + MS + MS:1000225 + This child of the former purgatory term ion attribute was made obsolete. + monoisotopic mass + true + + + + + OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam. + MBMS + MS + MS:1000226 + This child of the former purgatory term mass spectrometer was made obsolete. + molecular beam mass spectrometry + true + + + + + OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam. + PSI:MS + + + + + + + + + Photoionization of an atom or molecule in which in two or more photons are absorbed. + MPI + MS + MS:1000227 + multiphoton ionization + + + + + Photoionization of an atom or molecule in which in two or more photons are absorbed. + PSI:MS + + + + + + + + OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms. + MS + MS:1000228 + This child of the former purgatory term ion reaction was made obsolete. + nitrogen rule + true + + + + + OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms. + PSI:MS + + + + + + + + + + + + + + + + + + + + OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value. + MS + MS:1000229 + This child of the former purgatory term ion attribute was made obsolete. + nominal mass + true + + + + + OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value. + PSI:MS + + + + + + + + OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions. + MS + MS:1000230 + This child of the former purgatory term ion reaction was made obsolete. + odd-electron rule + true + + + + + OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions. + PSI:MS + + + + + + + + + + + + + + A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably. + MS + MS:1000231 + peak + + + + + A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably. + PSI:MS + + + + + + + + OBSOLETE The height or area of a peak in a mass spectrum. + MS + MS:1000232 + This term was made obsolete because it was replaced by base peak intensity (MS:1000505). + peak intensity + true + + + + + OBSOLETE The height or area of a peak in a mass spectrum. + PSI:MS + + + + + + + + + + + + + + OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states. + PA + MS + MS:1000233 + This child of the former purgatory term ion attribute was made obsolete. + proton affinity + true + + + + + OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states. + PSI:MS + + + + + PA + PSI:MS + + + + + + + + + + + + + + OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported. + MS + MS:1000234 + This term was made obsolete because it was replaced by mass resolving power (MS:1000800). + mass resolving power + true + + + + + OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported. + PSI:MS + + + + + + + + + Representation of the total ion current detected in each of a series of mass spectra versus time. + TIC chromatogram + MS + MS:1000235 + total ion current chromatogram + + + + + Representation of the total ion current detected in each of a series of mass spectra versus time. + PSI:MS + + + + + + + + + + + + + + + The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region. + MS + MS:1000236 + transmission + + + + + The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region. + PSI:MS + + + + + + + + OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg. + u + MS + MS:1000237 + This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221). + unified atomic mass unit + true + + + + + OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy. + AMS + MS + MS:1000238 + This child of the former purgatory term mass spectrometer was made obsolete. + accelerator mass spectrometry + true + + + + + OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy. + PSI:MS + + + + + + + + + Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer. + AP MALDI + MS + MS:1000239 + atmospheric pressure matrix-assisted laser desorption ionization + + + + + Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer. + PSI:MS + + + + + + + + + Any ionization process in which ions are formed in the gas phase at atmospheric pressure. + API + MS + MS:1000240 + atmospheric pressure ionization + + + + + Any ionization process in which ions are formed in the gas phase at atmospheric pressure. + PSI:MS + + + + + + + + OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. + APPI + MS + MS:1000241 + This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382). + Atmostpheric Pressure Photoionization + true + + + + + OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. + PSI:MS + + + + + + + + + A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation. + BIRD + MS + MS:1000242 + blackbody infrared radiative dissociation + + + + + A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation. + PSI:MS + + + + + + + + OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site. + CRF + MS + MS:1000243 + This child of the former purgatory term ion reaction was made obsolete. + charge-remote fragmentation + true + + + + + OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site. + PSI:MS + + + + + + + + OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. + CRM + MS + MS:1000244 + This former purgatory term was made obsolete. + consecutive reaction monitoring + true + + + + + OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. + PSI:MS + + + + + + + + + The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion. + CS + MS + MS:1000245 + charge stripping + + + + + The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion. + PSI:MS + + + + + + + + + The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer. + DE + MS + MS:1000246 + delayed extraction + + + + + The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer. + PSI:MS + + + + + + + + + The formation of ions from a solid or liquid material after the rapid vaporization of that sample. + DI + MS + MS:1000247 + desorption ionization + + + + + The formation of ions from a solid or liquid material after the rapid vaporization of that sample. + PSI:MS + + + + + + + + + A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization. + DIP + MS + MS:1000248 + direct insertion probe + + + + + A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization. + PSI:MS + + + + + + + + + The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization. + DLI + MS + MS:1000249 + direct liquid introduction + + + + + The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization. + PSI:MS + + + + + + + + + A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments. + ECD + MS + MS:1000250 + electron capture dissociation + + + + + A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments. + PSI:MS + + + + + + + + OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state. + EE + MS + MS:1000251 + This child of the former purgatory term ion chemical type was made obsolete. + even-electron ion + true + + + + + OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state. + PSI:MS + + + + + + + + OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion. + EIEIO + MS + MS:1000252 + This child of the former purgatory term ion reaction was made obsolete. + electron-induced excitation in organics + true + + + + + OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion. + PSI:MS + + + + + + + + + A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons. + EM + MS + MS:1000253 + electron multiplier + + + + + A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons. + PSI:MS + + + + + + + + + A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time. + ESA + MS + MS:1000254 + electrostatic energy analyzer + + + + + A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time. + PSI:MS + + + + + + + + + An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa. + FA + MS + MS:1000255 + flowing afterglow + + + + + An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa. + PSI:MS + + + + + + + + OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion. + FAIMS + MS + MS:1000256 + This child of the former purgatory term mass spectrometer was made obsolete. + high-field asymmetric waveform ion mobility spectrometry + true + + + + + OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion. + PSI:MS + + + + + + + + + The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization. + FD + MS + MS:1000257 + field desorption + + + + + The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization. + PSI:MS + + + + + + + + + The removal of electrons from any species by interaction with a high electric field. + FI + MS + MS:1000258 + field ionization + + + + + The removal of electrons from any species by interaction with a high electric field. + PSI:MS + + + + + + + + + The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas. + GD-MS + MS + MS:1000259 + glow discharge ionization + + + + + The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas. + PSI:MS + + + + + + + + OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge. + IKES + MS + MS:1000260 + This child of the former purgatory term mass spectrometer was made obsolete. + ion kinetic energy spectrometry + true + + + + + OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge. + PSI:MS + + + + + + + + OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field. + IMS + MS + MS:1000261 + This child of the former purgatory term mass spectrometer was made obsolete. + ion mobility spectrometry + true + + + + + OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field. + PSI:MS + + + + + + + + + Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons. + IRMPD + MS + MS:1000262 + infrared multiphoton dissociation + + + + + Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons. + PSI:MS + + + + + + + + OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer. + IRMS + MS + MS:1000263 + This child of the former purgatory term mass spectrometry was made obsolete. + isotope ratio mass spectrometry + true + + + + + OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer. + PSI:MS + + + + + + + + + A device for spatially confining ions using electric and magnetic fields alone or in combination. + IT + MS + MS:1000264 + ion trap + + + + + A device for spatially confining ions using electric and magnetic fields alone or in combination. + PSI:MS + + + + + + + + OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction. + KERD + MS + MS:1000265 + This child of the former purgatory term ion reaction was made obsolete. + kinetic energy release distribution + true + + + + + OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction. + PSI:MS + + + + + + + + OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules. + MS:1000393 + LD + Laser Ionization MERGE + MS + MS:1000266 + This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393). + Laser Desorption + true + + + + + OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules. + PSI:MS + + + + + + + + OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process. + MIKES + MS + MS:1000267 + This child of the former purgatory term mass spectrometer was made obsolete. + mass analyzed ion kinetic energy spectrometry + true + + + + + OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process. + PSI:MS + + + + + + + + OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments. + MS + MS + MS:1000268 + This former purgatory term was made obsolete. + mass spectrometry + true + + + + + OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments. + PSI:MS + + + + + + + + OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions. + MS/MS + MS + MS:1000269 + This child of the former purgatory term mass spectrometer was made obsolete. + mass spectrometry/mass spectrometry + true + + + + + OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions. + PSI:MS + + + + + + + + OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions. + MSn + MS + MS:1000270 + This child of the former purgatory term m/z Separation Method was made obsolete. + multiple stage mass spectrometry + true + + + + + OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions. + PSI:MS + + + + + + + + + Chemical ionization that results in the formation of negative ions. + NICI + MS + MS:1000271 + Negative Ion chemical ionization + + + + + Chemical ionization that results in the formation of negative ions. + PSI:MS + + + + + + + + + With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species. + NRMS + MS + MS:1000272 + neutralization reionization mass spectrometry + + + + + With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species. + PSI:MS + + + + + + + + + The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended. + PI + MS + MS:1000273 + photoionization + + + + + The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended. + PSI:MS + + + + + + + + + A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source. + PyMS + MS + MS:1000274 + pyrolysis mass spectrometry + + + + + A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source. + PSI:MS + + + + + + + + + A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation. + q + MS + MS:1000275 + collision quadrupole + + + + + A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation. + PSI:MS + + + + + + + + + Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species. + REMPI + MS + MS:1000276 + resonance enhanced multiphoton ionization + + + + + Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber. + RGA + MS + MS:1000277 + This child of the former purgatory term mass spectrometer was made obsolete. + residual gas analyzer + true + + + + + OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber. + PSI:MS + + + + + + + + + The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization. + SELDI + MS + MS:1000278 + surface enhanced laser desorption ionization + + + + + The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization. + PSI:MS + + + + + + + + + Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface. + SEND + MS + MS:1000279 + surface enhanced neat desorption + + + + + Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface. + PSI:MS + + + + + + + + OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. + SI + MS + MS:1000280 + This term was made obsolete because it was replaced by surface ionization (MS:1000406). + suface ionization + true + + + + + OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. + PSI:MS + + + + + + + + + A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions. + SIFT + MS + MS:1000281 + selected ion flow tube + + + + + A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions. + PSI:MS + + + + + + + + + A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time. + SORI + MS + MS:1000282 + sustained off-resonance irradiation + + + + + A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time. + PSI:MS + + + + + + + + OBSOLETE Mass spectrometry using spark ionization. + SSMS + MS + MS:1000283 + This term was made obsolete because it was replaced by spark ionization (MS:1000404). + Spark Source Mass Spectrometry + true + + + + + OBSOLETE Mass spectrometry using spark ionization. + PSI:MS + + + + + + + + + A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments. + SWIFT + MS + MS:1000284 + stored waveform inverse fourier transform + + + + + A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments. + PSI:MS + + + + + + + + + + + + + + + The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum. + TIC + MS + MS:1000285 + total ion current + + + + + The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum. + PSI:MS + + + + + + + + + Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse. + TLF + MS + MS:1000286 + time lag focusing + + + + + Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse. + PSI:MS + + + + + + + + OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy. + TOF-MS + MS + MS:1000287 + This child of the former purgatory term mass spectrometer was made obsolete. + time-of-flight mass spectrometer + true + + + + + OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy. + PSI:MS + + + + + + + + + A device that uses an oscillating electric field and magnetic field to accelerate charged particles. + MS + MS:1000288 + cyclotron + + + + + A device that uses an oscillating electric field and magnetic field to accelerate charged particles. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam. + MS + MS:1000289 + This child of the former purgatory term mass spectrometer was made obsolete. + double-focusing mass spectrometer + true + + + + + OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry. + MS + MS:1000290 + This child of the former purgatory term mass spectrometer was made obsolete. + hybrid mass spectrometer + true + + + + + OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry. + PSI:MS + + + + + + + + + A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap. + MS + MS:1000291 + linear ion trap + + + + + A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap. + PSI:MS + + + + + + + + OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate. + MS + MS:1000292 + This former purgatory term was made obsolete. + mass spectrograph obsolete + true + + + + + OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate. + PSI:MS + + + + + + + + OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions. + MS + MS:1000293 + This former purgatory term was made obsolete. + mass spectrometer + true + + + + + OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions. + PSI:MS + + + + + + + + + + A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z). + MS + MS:1000294 + mass spectrum + + + + + A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z). + PSI:MS + + + + + + + + OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians. + MS + MS:1000295 + This former purgatory term was made obsolete. + mattauch-herzog geometry + true + + + + + OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians. + PSI:MS + + + + + + + + OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians. + MS + MS:1000296 + This former purgatory term was made obsolete. + nier-johnson geometry + true + + + + + OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians. + PSI:MS + + + + + + + + OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected. + MS + quadrupole ion trap + MS:1000297 + This term was made obsolete because it is redundant to quadrupole ion trap. + paul ion trap + true + + + + + OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path. + MS + MS:1000298 + This child of the former purgatory term mass spectrometer was made obsolete. + prolate traochoidal mass spectrometer + true + + + + + OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path. + PSI:MS + + + + + + + + OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term. + MS + MS:1000299 + This former purgatory term was made obsolete. + quistor + true + + + + + OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term. + PSI:MS + + + + + + + + + A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time. + MS + MS:1000300 + reflectron + + + + + A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection. + MS + MS:1000301 + This child of the former purgatory term mass spectrometer was made obsolete. + sector mass spectrometer + true + + + + + OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry. + MS + MS:1000302 + This child of the former purgatory term mass spectrometer was made obsolete. + tandem mass spectrometer + true + + + + + OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. + MS + MS:1000303 + This child of the former purgatory term mass spectrometer was made obsolete. + transmission quadrupole mass spectrometer + true + + + + + OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The electrical potential used to impart kinetic energy to ions in a mass spectrometer. + MS + MS:1000304 + accelerating voltage + + + + + The electrical potential used to impart kinetic energy to ions in a mass spectrometer. + PSI:MS + + + + + + + + OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB. + MS + MS:1000305 + This child of the former purgatory term m/z Separation Method was made obsolete. + cyclotron motion + true + + + + + OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB. + PSI:MS + + + + + + + + OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time. + MS + MS:1000306 + This child of the former purgatory term mass spectrometer was made obsolete. + dynamic mass spectrometry + true + + + + + OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time. + PSI:MS + + + + + + + + + Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle. + MS + MS:1000307 + einzel lens + + + + + Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The magnitude of the force per unit charge at a given point in space. + MS + MS:1000308 + electric field strength + + + + + The magnitude of the force per unit charge at a given point in space. + PSI:MS + + + + + + + + + The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole. + MS + MS:1000309 + first stability region + + + + + The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole. + PSI:MS + + + + + + + + + The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element. + MS + MS:1000310 + fringing field + + + + + The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element. + PSI:MS + + + + + + + + + A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field. + MS + MS:1000311 + kinetic energy analyzer + + + + + A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field. + PSI:MS + + + + + + + + OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer. + MS + MS:1000312 + This former purgatory term was made obsolete. + mass limit + true + + + + + OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer. + PSI:MS + + + + + + + + OBSOLETE The limit of m/z over which a mass spectrometer can detect ions. + MS + MS:1000313 + This former purgatory term was made obsolete. + scan m/z range? + true + + + + + OBSOLETE The limit of m/z over which a mass spectrometer can detect ions. + PSI:MS + + + + + + + + OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap. + MS + MS:1000314 + This child of the former purgatory term m/z Separation Method was made obsolete. + mass selective axial ejection + true + + + + + OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap. + PSI:MS + + + + + + + + OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap. + MS + MS:1000315 + This child of the former purgatory term m/z Separation Method was made obsolete. + mass selective instability + true + + + + + OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap. + PSI:MS + + + + + + + + OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer. + MS + MS:1000316 + This child of the former purgatory term m/z Separation Method was made obsolete. + mathieu stability diagram + true + + + + + OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer. + PSI:MS + + + + + + + + OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage. + MS + MS:1000317 + This child of the former purgatory term m/z Separation Method was made obsolete. + orthogonal extraction + true + + + + + OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage. + PSI:MS + + + + + + + + OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it. + MS + MS:1000318 + This child of the former purgatory term m/z Separation Method was made obsolete. + resonance ion ejection + true + + + + + OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it. + PSI:MS + + + + + + + + + The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time. + MS + MS:1000319 + space charge effect + + + + + The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time. + PSI:MS + + + + + + + + + An electric or magnetic field that does not change in time. + MS + MS:1000320 + static field + + + + + An electric or magnetic field that does not change in time. + PSI:MS + + + + + + + + OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained. + MS + MS:1000321 + This child of the former purgatory term m/z Separation Method was made obsolete. + 2E Mass Spectrum + true + + + + + OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained. + PSI:MS + + + + + + + + + The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z. + MS + MS:1000322 + charge inversion mass spectrum + + + + + The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z. + PSI:MS + + + + + + + + OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement. + MS + constant neutral mass loss scan + fixed neutral fragment scan + MS:1000323 + This former purgatory term was made obsolete. + constant neutral loss scan + true + + + + + OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement. + PSI:MS + + + + + + + + OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment. + Constant Neutral Mass Gain Scan + MS + MS:1000324 + This former purgatory term was made obsolete. + constant neutral gain scan + true + + + + + OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment. + PSI:MS + + + + + + + + + A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell. + constant neutral mass gain spectrum + MS + MS:1000325 + constant neutral gain spectrum + + + + + A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell. + PSI:MS + + + + + + + + + A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. + constant neutral mass loss spectrum + MS + MS:1000326 + constant neutral loss spectrum + + + + + A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum. + PSI:MS + + + + + + + + OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. + MS + MS:1000327 + This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244). + consecutive reaction monitoring + true + + + + + OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. + PSI:MS + + + + + + + + + A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions. + MS + MS:1000328 + e/2 mass spectrum + + + + + A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions. + PSI:MS + + + + + + + + OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum. + MS + MS:1000329 + This former purgatory term was made obsolete. + linked scan + true + + + + + OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum. + PSI:MS + + + + + + + + OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. + MS + MS:1000330 + This child of the former purgatory term linked scan was made obsolete. + linked scan at constant b/e + true + + + + + OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. + PSI:MS + + + + + + + + OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors. + MS + MS:1000331 + This child of the former purgatory term linked scan was made obsolete. + Linked Scan at Constant E2/V + true + + + + + OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors. + PSI:MS + + + + + + + + OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended. + MS + MS:1000332 + This child of the former purgatory term linked scan was made obsolete. + Linked Scan at Constant B2/E + true + + + + + OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended. + PSI:MS + + + + + + + + OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan. + MS + MS:1000333 + This child of the former purgatory term linked scan was made obsolete. + Linked Scan at Constant B[1-(E/E0)]^1/2 / E + true + + + + + OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan. + PSI:MS + + + + + + + + OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time. + MS + MS:1000334 + This child of the former purgatory term m/z Separation Method was made obsolete. + MS/MS in Time + true + + + + + OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time. + PSI:MS + + + + + + + + OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition. + MS + MS:1000335 + This child of the former purgatory term m/z Separation Method was made obsolete. + MS/MS in Space + true + + + + + OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition. + PSI:MS + + + + + + + + + + + + + + + The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type). + MS + MS:1000336 + neutral loss + + + + + The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type). + PSI:MS + + + + + + + + OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated. + MS + granddaughter ion + MS:1000337 + This child of the former purgatory term product ion was made obsolete. + nth generation product ion + true + + + + + OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated. + PSI:MS + + + + + + + + OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions. + MS + MS:1000338 + This former purgatory term was made obsolete. + nth generation product ion scan + true + + + + + OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions. + PSI:MS + + + + + + + + OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions. + MS + MS:1000339 + This term was made obsolete because it was merged with MSn spectrum (MS:1000580). + nth generation product ion spectrum + true + + + + + OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions. + PSI:MS + + + + + + + + OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated. + MS + parent ion + MS:1000340 + This child of the former purgatory term ion role was made obsolete. + precursor ion + true + + + + + OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated. + PSI:MS + + + + + + + + + Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z. + MS + MS:1000341 + precursor ion spectrum + + + + + Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z. + PSI:MS + + + + + + + + OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated. + MS + daughter ion + MS:1000342 + This child of the former purgatory term ion role was made obsolete. + product ion + true + + + + + OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated. + PSI:MS + + + + + + + + + OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions. + MS + MS:1000343 + This term was made obsolete because it was merged with MSn spectrum (MS:1000580). + product ion spectrum + true + + + + + OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions. + PSI:MS + + + + + + + + OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+. + Progeny Fragment Ion + MS + MS:1000344 + This child of the former purgatory term ion chemical type was made obsolete. + progeny ion + true + + + + + OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+. + PSI:MS + + + + + + + + + Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector. + MS + MS:1000345 + array detector + + + + + Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector. + PSI:MS + + + + + + + + + A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected. + MS + MS:1000346 + conversion dynode + + + + + A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected. + PSI:MS + + + + + + + + + One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode. + MS + MS:1000347 + dynode + + + + + One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode. + PSI:MS + + + + + + + + + A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. + MS + MS:1000348 + focal plane collector + + + + + A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane. + PSI:MS + + + + + + + + + A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier. + MS + MS:1000349 + ion-to-photon detector + + + + + A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier. + PSI:MS + + + + + + + + + A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially. + MS + MS:1000350 + point collector + + + + + A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially. + PSI:MS + + + + + + + + + A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector. + MS + MS:1000351 + postacceleration detector + + + + + A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector. + PSI:MS + + + + + + + + OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go. + MS + MS:1000352 + This former purgatory term was made obsolete. + secondary electron + true + + + + + OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go. + PSI:MS + + + + + + + + + Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules. + MS + MS:1000353 + adduct ion + + + + + Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules. + PSI:MS + + + + + + + + OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure. + MS + MS:1000354 + This child of the former purgatory term ion chemical type was made obsolete. + aromatic ion + true + + + + + OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure. + PSI:MS + + + + + + + + OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+. + MS + MS:1000355 + This child of the former purgatory term ion chemical type was made obsolete. + analog ion + true + + + + + OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+. + PSI:MS + + + + + + + + OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic. + MS + MS:1000356 + This child of the former purgatory term ion chemical type was made obsolete. + anti-aromatic ion + true + + + + + OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic. + PSI:MS + + + + + + + + OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used. + MS + MS:1000357 + This child of the former purgatory term ion chemical type was made obsolete. + cationized molecule + true + + + + + OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used. + PSI:MS + + + + + + + + OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-. + MS + MS:1000358 + This child of the former purgatory term ion chemical type was made obsolete. + cluster ion + true + + + + + OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-. + PSI:MS + + + + + + + + OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion. + MS + MS:1000359 + This child of the former purgatory term ion chemical type was made obsolete. + Conventional ion + true + + + + + OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion. + PSI:MS + + + + + + + + OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives. + MS + MS:1000360 + This child of the former purgatory term ion chemical type was made obsolete. + diagnostic ion + true + + + + + OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives. + PSI:MS + + + + + + + + OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+. + MS + MS:1000361 + This child of the former purgatory term ion chemical type was made obsolete. + dimeric ion + true + + + + + OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+. + PSI:MS + + + + + + + + OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion. + MS + MS:1000362 + This child of the former purgatory term ion chemical type was made obsolete. + distonic ion + true + + + + + OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion. + PSI:MS + + + + + + + + OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions. + MS + MS:1000363 + This child of the former purgatory term ion chemical type was made obsolete. + enium ion + true + + + + + OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions. + PSI:MS + + + + + + + + OBSOLETE A product ion that results from the dissociation of a precursor ion. + MS + MS:1000364 + This term was made obsolete because it was replaced by product ion (MS:1000342). + fragment ion + true + + + + + OBSOLETE A product ion that results from the dissociation of a precursor ion. + PSI:MS + + + + + + + + OBSOLETE An atomic or molecular species having a net positive or negative electric charge. + MS + MS:1000365 + This former purgatory term was made obsolete. + ion? + true + + + + + OBSOLETE An atomic or molecular species having a net positive or negative electric charge. + PSI:MS + + + + + + + + OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue. + MS + MS:1000366 + This child of the former purgatory term ion chemical type was made obsolete. + Isotopologue ion + true + + + + + OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue. + PSI:MS + + + + + + + + OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer. + MS + MS:1000367 + This child of the former purgatory term ion chemical type was made obsolete. + Isotopomeric ion + true + + + + + OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer. + PSI:MS + + + + + + + + OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection. + MS + MS:1000368 + This child of the former purgatory term ion stability type was made obsolete. + metastable ion + true + + + + + OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection. + PSI:MS + + + + + + + + OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion. + MS + MS:1000369 + This child of the former purgatory term ion chemical type was made obsolete. + molecular ion + true + + + + + OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion. + PSI:MS + + + + + + + + OBSOLETE An atomic or molecular species having a net negative electric charge. + MS + MS:1000370 + This child of the former purgatory term ion chemical type was made obsolete. + negative ion + true + + + + + OBSOLETE An atomic or molecular species having a net negative electric charge. + PSI:MS + + + + + + + + OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions. + MS + MS:1000371 + This child of the former purgatory term ion chemical type was made obsolete. + non-classical ion + true + + + + + OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions. + PSI:MS + + + + + + + + OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+. + MS + MS:1000372 + This child of the former purgatory term ion chemical type was made obsolete. + onium ion + true + + + + + OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+. + PSI:MS + + + + + + + + OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions. + MS + MS:1000373 + This child of the former purgatory term ion chemical type was made obsolete. + principal ion + true + + + + + OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions. + PSI:MS + + + + + + + + OBSOLETE An atomic or molecular species having a net positive electric charge. + MS + MS:1000374 + This child of the former purgatory term ion chemical type was made obsolete. + positive ion + true + + + + + OBSOLETE An atomic or molecular species having a net positive electric charge. + PSI:MS + + + + + + + + OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended. + MS + MS:1000375 + This child of the former purgatory term ion chemical type was made obsolete. + protonated molecule + true + + + + + OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended. + PSI:MS + + + + + + + + OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation. + MS + MS:1000376 + This child of the former purgatory term ion chemical type was made obsolete. + radical ion + true + + + + + OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation. + PSI:MS + + + + + + + + OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion. + MS + MS:1000377 + This child of the former purgatory term ion chemical type was made obsolete. + reference ion + true + + + + + OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion. + PSI:MS + + + + + + + + OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer. + MS + MS:1000378 + This child of the former purgatory term ion stability type was made obsolete. + stable ion + true + + + + + OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer. + PSI:MS + + + + + + + + OBSOLETE An ion with sufficient energy to dissociate within the ion source. + MS + MS:1000379 + This child of the former purgatory term ion stability type was made obsolete. + unstable ion + true + + + + + OBSOLETE An ion with sufficient energy to dissociate within the ion source. + PSI:MS + + + + + + + + + A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state. + MS + MS:1000380 + adiabatic ionization + + + + + A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state. + PSI:MS + + + + + + + + + An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron. + MS + MS:1000381 + associative ionization + + + + + An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron. + PSI:MS + + + + + + + + + Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. + MS + MS:1000382 + atmospheric pressure photoionization + + + + + Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization. + PSI:MS + + + + + + + + + The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source. + MS + MS:1000383 + autodetachment + + + + + The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source. + PSI:MS + + + + + + + + + The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source. + MS + MS:1000384 + autoionization + + + + + The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source. + PSI:MS + + + + + + + + + The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization. + MS + MS:1000385 + charge exchange ionization + + + + + The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization. + PSI:MS + + + + + + + + + The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization. + MS + MS:1000386 + chemi-ionization + + + + + The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization. + PSI:MS + + + + + + + + + The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface. + MS + MS:1000387 + desorption/ionization on silicon + + + + + The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface. + PSI:MS + + + + + + + + + The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion. + MS + MS:1000388 + dissociative ionization + + + + + The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion. + PSI:MS + + + + + + + + + The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. + MS + MS:1000389 + electron ionization + + + + + The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. + PSI:MS + + + + + + + + OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules. + MS + MS:1000390 + This child of the former purgatory term ion reaction was made obsolete. + ion desolvation + true + + + + + OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules. + PSI:MS + + + + + + + + OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products. + MS + MS:1000391 + This child of the former purgatory term ion reaction was made obsolete. + ion-pair formation + true + + + + + OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products. + PSI:MS + + + + + + + + + + + + + + + The ratio of the number of ions formed to the number of electrons, molecules or photons used. + MS + MS:1000392 + ionization efficiency + + + + + The ratio of the number of ions formed to the number of electrons, molecules or photons used. + PSI:MS + + + + + + + + + The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material. + MS + MS:1000393 + laser desorption ionization + + + + + The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material. + PSI:MS + + + + + + + + + The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization. + MS + MS:1000395 + liquid secondary ionization + + + + + The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization. + PSI:MS + + + + + + + + + A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source. + MS + MS:1000396 + membrane inlet + + + + + A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source. + PSI:MS + + + + + + + + + Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray. + MS + MS:1000397 + microelectrospray + + + + + Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray. + PSI:MS + + + + + + + + + Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray. + nanospray + MS + MS:1000398 + nanoelectrospray + + + + + Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray. + PSI:MS + + + + + + + + + Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited. + MS + MS:1000399 + penning ionization + + + + + Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited. + PSI:MS + + + + + + + + + The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. + MS + MS:1000400 + plasma desorption ionization + + + + + The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization. + PSI:MS + + + + + + + + OBSOLETE An electronic state capable of undergoing auto-Ionization. + MS + MS:1000401 + This child of the former purgatory term ion reaction was made obsolete. + pre-ionization state + true + + + + + OBSOLETE An electronic state capable of undergoing auto-Ionization. + PSI:MS + + + + + + + + + The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions. + MS + MS:1000402 + secondary ionization + + + + + The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions. + PSI:MS + + + + + + + + + The formation of gas-phase ions without extensive fragmentation. + MS + MS:1000403 + soft ionization + + + + + The formation of gas-phase ions without extensive fragmentation. + PSI:MS + + + + + + + + + The formation of ions from a solid material by an intermittent electrical discharge. + MS + MS:1000404 + spark ionization + + + + + The formation of ions from a solid material by an intermittent electrical discharge. + PSI:MS + + + + + + + + + The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization. + MS + MS:1000405 + surface-assisted laser desorption ionization + + + + + The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization. + PSI:MS + + + + + + + + + The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. + MS + MS:1000406 + surface ionization + + + + + The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature. + PSI:MS + + + + + + + + + The ionization of a neutral species through contact with a high temperature surface. + MS + MS:1000407 + thermal ionization + + + + + The ionization of a neutral species through contact with a high temperature surface. + PSI:MS + + + + + + + + + A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state. + MS + MS:1000408 + vertical ionization + + + + + A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state. + PSI:MS + + + + + + + + OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion. + MS + MS:1000409 + This child of the former purgatory term ion reaction was made obsolete. + association reaction + true + + + + + OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion. + PSI:MS + + + + + + + + OBSOLETE A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds. + MS + MS:1000410 + This child of the former purgatory term ion reaction was made obsolete. + alpha-cleavage + true + + + + + OBSOLETE A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds. + PSI:MS + + + + + + + + OBSOLETE A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds. + MS + MS:1000411 + This child of the former purgatory term ion reaction was made obsolete. + beta-cleavage + true + + + + + OBSOLETE A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds. + PSI:MS + + + + + + + + + + + + + + + An inert gas used for collisional deactivation of internally excited ions. + MS + MS:1000412 + buffer gas + + + + + An inert gas used for collisional deactivation of internally excited ions. + PSI:MS + + + + + + + + OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation. + MS + MS:1000413 + This child of the former purgatory term ion reaction was made obsolete. + charge-induced fragmentation + true + + + + + OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation. + PSI:MS + + + + + + + + OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion. + MS + MS:1000414 + This child of the former purgatory term ion reaction was made obsolete. + charge inversion reaction + true + + + + + OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion. + PSI:MS + + + + + + + + OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion. + MS + MS:1000415 + This child of the former purgatory term ion reaction was made obsolete. + charge permutation reaction + true + + + + + OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion. + PSI:MS + + + + + + + + OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion. + MS + MS:1000416 + This child of the former purgatory term ion reaction was made obsolete. + charge stripping reaction + true + + + + + OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion. + PSI:MS + + + + + + + + OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species. + MS + MS:1000417 + This child of the former purgatory term ion reaction was made obsolete. + charge transfer reaction + true + + + + + OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species. + PSI:MS + + + + + + + + OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion. + MS + MS:1000418 + This child of the former purgatory term ion reaction was made obsolete. + collisional excitation + true + + + + + OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion. + PSI:MS + + + + + + + + + + + + + + + An inert gas used for collisional excitation. The term target gas is not recommended. + MS + MS:1000419 + collision gas + + + + + An inert gas used for collisional excitation. The term target gas is not recommended. + PSI:MS + + + + + + + + OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis. + MS + heterolysis + MS:1000420 + This child of the former purgatory term ion reaction was made obsolete. + heterolytic cleavage + true + + + + + OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis. + PSI:MS + + + + + + + + OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV. + MS + MS:1000421 + This child of the former purgatory term ion reaction was made obsolete. + high energy collision + true + + + + + OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV. + PSI:MS + + + + + + + + + A collision-induced dissociation process that occurs in a beam-type collision cell. + HCD + MS + MS:1000422 + beam-type collision-induced dissociation + + + + + A collision-induced dissociation process that occurs in a beam-type collision cell. + PSI:MS + + + + + + + + OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis. + MS + homolysis + MS:1000423 + This child of the former purgatory term ion reaction was made obsolete. + homolytic cleavage + true + + + + + OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis. + PSI:MS + + + + + + + + OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer. + MS + MS:1000424 + This child of the former purgatory term ion reaction was made obsolete. + hydrogen/deuterium exchange + true + + + + + OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer. + PSI:MS + + + + + + + + OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species. + MS + MS:1000425 + This former purgatory term was made obsolete. + ion energy loss spectrum + true + + + + + OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species. + PSI:MS + + + + + + + + OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral. + MS + MS:1000426 + This child of the former purgatory term ion reaction was made obsolete. + ionizing collision + true + + + + + OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral. + PSI:MS + + + + + + + + OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule. + MS + MS:1000427 + This child of the former purgatory term ion reaction was made obsolete. + ion/molecule reaction + true + + + + + OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule. + PSI:MS + + + + + + + + OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions. + MS + MS:1000428 + This child of the former purgatory term ion reaction was made obsolete. + ion/neutral complex + true + + + + + OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions. + PSI:MS + + + + + + + + OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants. + MS + MS:1000429 + This child of the former purgatory term ion reaction was made obsolete. + ion/neutral species reaction + true + + + + + OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants. + PSI:MS + + + + + + + + OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product. + MS + MS:1000430 + This child of the former purgatory term ion reaction was made obsolete. + ion/neutral species exchange reaction + true + + + + + OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product. + PSI:MS + + + + + + + + OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account. + MS + MS:1000431 + This child of the former purgatory term ion reaction was made obsolete. + kinetic method + true + + + + + OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account. + PSI:MS + + + + + + + + OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower. + MS + MS:1000432 + This child of the former purgatory term ion reaction was made obsolete. + low energy collisions + true + + + + + OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower. + PSI:MS + + + + + + + + + A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative. + MS + MS:1000433 + low-energy collision-induced dissociation + + + + + A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative. + PSI:MS + + + + + + + + OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied. + MS + MS:1000434 + This child of the former purgatory term ion reaction was made obsolete. + McLafferty Rearrangement + true + + + + + OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied. + PSI:MS + + + + + + + + + A process wherein the reactant ion is dissociated as a result of absorption of one or more photons. + MPD + multiphoton dissociation + MS + MS:1000435 + photodissociation + + + + + A process wherein the reactant ion is dissociated as a result of absorption of one or more photons. + PSI:MS + + + + + + + + OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral. + MS + MS:1000436 + This child of the former purgatory term ion reaction was made obsolete. + partial charge transfer reaction + true + + + + + OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral. + PSI:MS + + + + + + + + OBSOLETE Chemical transformation involving an ion. + MS + MS:1000437 + This child of the former purgatory term ion was made obsolete. + ion reaction + true + + + + + OBSOLETE Chemical transformation involving an ion. + PSI:MS + + + + + + + + OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners. + MS + MS:1000438 + This child of the former purgatory term ion reaction was made obsolete. + superelastic collision + true + + + + + OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners. + PSI:MS + + + + + + + + OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion. + MS + MS:1000439 + This child of the former purgatory term ion reaction was made obsolete. + surface-induced reaction + true + + + + + OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion. + PSI:MS + + + + + + + + OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion. + MS + MS:1000440 + This child of the former purgatory term ion reaction was made obsolete. + unimolecular dissociation + true + + + + + OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion. + PSI:MS + + + + + + + + + + + + + + Function or process of the mass spectrometer where it records a spectrum. + MS + MS:1000441 + scan + + + + + Function or process of the mass spectrometer where it records a spectrum. + PSI:MS + + + + + + + + + + + + + + Representation of intensity values corresponding to a range of measurement space. + MS + MS:1000442 + spectrum + + + + + Representation of intensity values corresponding to a range of measurement space. + PSI:MS + + + + + + + + + + + + + + Mass analyzer separates the ions according to their mass-to-charge ratio. + MS + MS:1000443 + mass analyzer type + + + + + Mass analyzer separates the ions according to their mass-to-charge ratio. + PSI:MS + + + + + + + + OBSOLETE Mass/charge separation Method. + MS + MS:1000444 + This former purgatory term was made obsolete. + m/z Separation Method + true + + + + + OBSOLETE Mass/charge separation Method. + PSI:MS + + + + + + + + OBSOLETE Sequential m/z separation method. + MS + MS:1000445 + This former purgatory term was made obsolete. + sequential m/z separation method + true + + + + + OBSOLETE Sequential m/z separation method. + PSI:MS + + + + + + + + + The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample. + FIB + MS + MS:1000446 + fast ion bombardment + + + + + The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample. + PSI:MS + + + + + + + + + Finnigan LTQ MS. + MS + MS:1000447 + LTQ + + + + + Finnigan LTQ MS. + PSI:MS + + + + + + + + + Finnigan LTQ FT MS. + MS + MS:1000448 + LTQ FT + + + + + Finnigan LTQ FT MS. + PSI:MS + + + + + + + + + Finnigan LTQ Orbitrap MS. + MS + MS:1000449 + LTQ Orbitrap + + + + + Finnigan LTQ Orbitrap MS. + PSI:MS + + + + + + + + + Finnigan LXQ MS. + MS + MS:1000450 + LXQ + + + + + Finnigan LXQ MS. + PSI:MS + + + + + + + + + + + + + + Terms used to describe the Analyzer. + analyzer + MS + MS:1000451 + mass analyzer + + + + + Terms used to describe the Analyzer. + PSI:MS + + + + + + + + + + + + + + Terms used to describe types of data processing. + data processing + MS + MS:1000452 + data transformation + + + + + Terms used to describe types of data processing. + PSI:MS + + + + + + + + + + + + + + The device that detects ions. + MS + MS:1000453 + detector + + + + + The device that detects ions. + PSI:MS + + + + + + + + OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5. + MS + MS:1000454 + This former purgatory term was made obsolete. + instrument additional description + true + + + + + OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5. + PSI:MS + + + + + + + + + + + + + + + Ion selection properties that are associated with a value. + MS + MS:1000455 + ion selection attribute + + + + + Ion selection properties that are associated with a value. + PSI:MS + + + + + + + + + + + + + + Terms to describe the precursor activation. + activation + MS + MS:1000456 + precursor activation + + + + + Terms to describe the precursor activation. + PSI:MS + + + + + + + + + + + + + + Terms to describe the sample. + MS + MS:1000457 + sample + + + + + Terms to describe the sample. + PSI:MS + + + + + + + + + + + + + + Terms to describe the source. + MS + MS:1000458 + source + + + + + Terms to describe the source. + PSI:MS + + + + + + + + OBSOLETE Terms used to describe the spectrum. + MS + MS:1000459 + This former purgatory term was made obsolete. + spectrum instrument description + true + + + + + OBSOLETE Terms used to describe the spectrum. + PSI:MS + + + + + + + + + + + + + + OBSOLETE Terms to describe units. + MS + MS:1000460 + This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000). + unit + true + + + + + OBSOLETE Terms to describe units. + PSI:MS + + + + + + + + OBSOLETE Terms to describe Additional. + MS + MS:1000461 + This former purgatory term was made obsolete. + additional description + true + + + + + OBSOLETE Terms to describe Additional. + PSI:MS + + + + + + + + + + + + + + Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions. + MS + MS:1000462 + ion optics + + + + + Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions. + PSI:MS + + + + + + + + + + + + + + Description of the instrument or the mass spectrometer. + instrument configuration + MS + MS:1000463 + instrument + + + + + Description of the instrument or the mass spectrometer. + PSI:MS + + + + + + + + OBSOLETE A unit of measurement for mass. + MS + MS:1000464 + This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002). + mass unit + true + + + + + OBSOLETE A unit of measurement for mass. + PSI:MS + + + + + + + + + + + + + + Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer. + MS + MS:1000465 + scan polarity + + + + + Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer. + PSI:MS + + + + + + + + OBSOLETE Alternating. + MS + MS:1000466 + This term was made obsolete because . + alternating + true + + + + + OBSOLETE Alternating. + PSI:MS + + + + + + + + + The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2. + MS + MS:1000467 + 1200 series LC/MSD SL + + + + + The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2. + PSI:MS + + + + + + + + + The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications. + MS + MS:1000468 + 6110 Quadrupole LC/MS + + + + + The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications. + PSI:MS + + + + + + + + + The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition. + MS + MS:1000469 + 6120A Quadrupole LC/MS + + + + + The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition. + PSI:MS + + + + + + + + + The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition. + MS + MS:1000470 + 6130 Quadrupole LC/MS + + + + + The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition. + PSI:MS + + + + + + + + + The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition. + MS + MS:1000471 + 6140 Quadrupole LC/MS + + + + + The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition. + PSI:MS + + + + + + + + + The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. + MS + MS:1000472 + 6210 Time-of-Flight LC/MS + + + + + The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. + PSI:MS + + + + + + + + + The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges. + MS + MS:1000473 + 6310 Ion Trap LC/MS + + + + + The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges. + PSI:MS + + + + + + + + + The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. + MS + MS:1000474 + 6320 Ion Trap LC/MS + + + + + The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. + PSI:MS + + + + + + + + + The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. + MS + MS:1000475 + 6330 Ion Trap LC/MS + + + + + The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. + PSI:MS + + + + + + + + + The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. + MS + MS:1000476 + 6340 Ion Trap LC/MS + + + + + The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges. + PSI:MS + + + + + + + + + The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration. + 6410 Triple Quad LC/MS + MS + MS:1000477 + 6410 Triple Quadrupole LC/MS + + + + + The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration. + PSI:MS + + + + + + + + + The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor. + MS + MS:1000478 + 1200 series LC/MSD VL + + + + + The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor. + PSI:MS + + + + + + + + OBSOLETE Terms that will likely become obsolete unless there are wails of dissent. + MS + MS:1000479 + The whole branch purgatory term was made obsolete. + purgatory + true + + + + + OBSOLETE Terms that will likely become obsolete unless there are wails of dissent. + PSI:MS + + + + + + + + + + + + + + Analyzer properties that are associated with a value. + MS + MS:1000480 + mass analyzer attribute + + + + + Analyzer properties that are associated with a value. + PSI:MS + + + + + + + + + + + + + + Detector attribute recognized as a value. + MS + MS:1000481 + detector attribute + + + + + Detector attribute recognized as a value. + PSI:MS + + + + + + + + + + + + + + Property of a source device that need a value. + MS + MS:1000482 + source attribute + + + + + Property of a source device that need a value. + PSI:MS + + + + + + + + + Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific. + MS + Thermo Scientific + MS:1000483 + Thermo Fisher Scientific instrument model + + + + + Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific. + PSI:MS + + + + + + + + + An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer. + MS + MS:1000484 + orbitrap + + + + + An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer. + PSI:MS + + + + + + + + + Nanospray Inlet. + MS + MS:1000485 + nanospray inlet + + + + + Nanospray Inlet. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Potential difference at the MS source in volts. + MS + MS:1000486 + source potential + + + + + Potential difference at the MS source in volts. + PSI:MS + + + + + + + + + Ion optics involves components that help focus ion streams in mass spectrometry. + MS + MS:1000487 + ion optics attribute + + + + + Ion optics involves components that help focus ion streams in mass spectrometry. + PSI:MS + + + + + + + + + Hitachi instrument model. + MS + MS:1000488 + Hitachi instrument model + + + + + Hitachi instrument model. + PSI:MS + + + + + + + + + Varian instrument model. + MS + MS:1000489 + Varian instrument model + + + + + Varian instrument model. + PSI:MS + + + + + + + + + Agilent instrument model. + MS + MS:1000490 + Agilent instrument model + + + + + Agilent instrument model. + PSI:MS + + + + + + + + + Dionex instrument model. + MS + MS:1000491 + Dionex instrument model + + + + + Dionex instrument model. + PSI:MS + + + + + + + + + Thermo Electron Corporation instrument model. + MS + MS:1000492 + Thermo Electron instrument model + + + + + Thermo Electron Corporation instrument model. + PSI:MS + + + + + + + + + Finnigan MAT instrument model. + MS + MS:1000493 + Finnigan MAT instrument model + + + + + Finnigan MAT instrument model. + PSI:MS + + + + + + + + + Thermo Scientific instrument model. + MS + MS:1000494 + Thermo Scientific instrument model + + + + + Thermo Scientific instrument model. + PSI:MS + + + + + + + + + Applied Biosystems instrument model. + ABI + MS + MS:1000495 + Applied Biosystems instrument model + + + + + Applied Biosystems instrument model. + PSI:MS + + + + + + + + + + + + + + + Instrument properties that are associated with a value. + MS + MS:1000496 + instrument attribute + + + + + Instrument properties that are associated with a value. + PSI:MS + + + + + + + + + Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate. + enhanced resolution scan + MS + MS:1000497 + zoom scan + + + + + Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate. + PSI:MS + + + + + + + + OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range. + MS + MS:1000498 + This former purgatory term was made obsolete. + full scan + true + + + + + OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range. + PSI:MS + + + + + + + + + + + + + + Nonphysical characteristic attributed to a spectrum. + MS + MS:1000499 + spectrum attribute + + + + + Nonphysical characteristic attributed to a spectrum. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The lower m/z bound of a mass spectrometer scan window. + MS + mzRangeStop + MS:1000500 + scan window upper limit + + + + + The lower m/z bound of a mass spectrometer scan window. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The upper m/z bound of a mass spectrometer scan window. + MS + mzRangeStart + MS:1000501 + scan window lower limit + + + + + The upper m/z bound of a mass spectrometer scan window. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The time spent gathering data across a peak. + MS + Scan Duration + MS:1000502 + dwell time + + + + + The time spent gathering data across a peak. + PSI:MS + + + + + + + + + + + + + + + Nonphysical characteristic attributed to a spectrum acquisition scan. + MS + MS:1000503 + scan attribute + + + + + Nonphysical characteristic attributed to a spectrum acquisition scan. + PSI:MS + + + + + + + + + + + + + + + + + + + + + M/z value of the signal of highest intensity in the mass spectrum. + MS + MS:1000504 + base peak m/z + + + + + M/z value of the signal of highest intensity in the mass spectrum. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The intensity of the greatest peak in the mass spectrum. + MS + MS:1000505 + base peak intensity + + + + + The intensity of the greatest peak in the mass spectrum. + PSI:MS + + + + + + + + OBSOLETE Ion Role. + MS + MS:1000506 + This child of the former purgatory term ion was made obsolete. + ion role + true + + + + + OBSOLETE Ion Role. + PSI:MS + + + + + + + + + + + + + + Nonphysical characteristic attributed to an ion. + MS + MS:1000507 + ion property + + + + + Nonphysical characteristic attributed to an ion. + PSI:MS + + + + + + + + OBSOLETE Ion Type. + MS + MS:1000508 + This child of the former purgatory term ion was made obsolete. + ion chemical type + true + + + + + OBSOLETE Ion Type. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Activation Energy. + MS + MS:1000509 + activation energy + + + + + Activation Energy. + PSI:MS + + + + + + + + + + + + + + Precursor Activation Attribute. + MS + MS:1000510 + precursor activation attribute + + + + + Precursor Activation Attribute. + PSI:MS + + + + + + + + + + + + + + + Stage number achieved in a multi stage mass spectrometry acquisition. + MS + MS:1000511 + ms level + + + + + Stage number achieved in a multi stage mass spectrometry acquisition. + PSI:MS + + + + + + + + + + + + + + + A string unique to Thermo instrument describing instrument settings for the scan. + MS + MS:1000512 + filter string + + + + + A string unique to Thermo instrument describing instrument settings for the scan. + PSI:MS + + + + + + + + + + + + + + + + + + + + A data array of values. + MS + MS:1000513 + binary data array + + + + + A data array of values. + PSI:MS + + + + + + + + + + + + + + + A data array of m/z values. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1000514 + m/z array + + + + + A data array of m/z values. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A data array of intensity values. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1000515 + intensity array + + + + + A data array of intensity values. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + A data array of charge values. + binary-data-type:MS:1000519 + MS + MS:1000516 + charge array + + + + + A data array of charge values. + PSI:MS + + + + + binary-data-type:MS:1000519 + 32-bit integer + + + + + + + + + A data array of signal-to-noise values. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1000517 + signal to noise array + + + + + A data array of signal-to-noise values. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + + + + + + + + + + + + Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float. + MS + MS:1000518 + binary data type + + + + + Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float. + PSI:MS + + + + + + + + + Signed 32-bit little-endian integer. + MS + MS:1000519 + 32-bit integer + + + + + Signed 32-bit little-endian integer. + PSI:MS + + + + + + + + + OBSOLETE Signed 16-bit float. + MS + MS:1000520 + 16-bit float + true + + + + + OBSOLETE Signed 16-bit float. + PSI:MS + + + + + + + + + 32-bit precision little-endian floating point conforming to IEEE-754. + MS + MS:1000521 + 32-bit float + + + + + 32-bit precision little-endian floating point conforming to IEEE-754. + PSI:MS + + + + + + + + + Signed 64-bit little-endian integer. + MS + MS:1000522 + 64-bit integer + + + + + Signed 64-bit little-endian integer. + PSI:MS + + + + + + + + + 64-bit precision little-endian floating point conforming to IEEE-754. + MS + MS:1000523 + 64-bit float + + + + + 64-bit precision little-endian floating point conforming to IEEE-754. + PSI:MS + + + + + + + + + + + + + + Describes the data content on the file. + MS + MS:1000524 + data file content + + + + + Describes the data content on the file. + PSI:MS + + + + + + + + + + + + + + Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks. + MS + MS:1000525 + spectrum representation + + + + + Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks. + PSI:MS + + + + + + + + + Waters data file format found in a Waters RAW directory, generated from an MS acquisition. + MS + MS:1000526 + Waters raw format + + + + + Waters data file format found in a Waters RAW directory, generated from an MS acquisition. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + Highest m/z value observed in the m/z array. + MS + MS:1000527 + highest observed m/z + + + + + Highest m/z value observed in the m/z array. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + Lowest m/z value observed in the m/z array. + MS + MS:1000528 + lowest observed m/z + + + + + Lowest m/z value observed in the m/z array. + PSI:MS + + + + + + + + + + + + + + + Serial Number of the instrument. + MS + MS:1000529 + instrument serial number + + + + + Serial Number of the instrument. + PSI:MS + + + + + + + + + Conversion of one file format to another. + MS + MS:1000530 + file format conversion + + + + + Conversion of one file format to another. + PSI:MS + + + + + + + + + + + + + + Software related to the recording or transformation of spectra. + MS + MS:1000531 + software + + + + + Software related to the recording or transformation of spectra. + PSI:MS + + + + + + + + + + + + Thermo Finnigan software for data acquisition and analysis. + MS + MS:1000532 + Xcalibur + + + + + Thermo Finnigan software for data acquisition and analysis. + PSI:MS + + + + + + + + + + + Thermo Finnigan software for data analysis of peptides and proteins. + MS + Bioworks Browser + MS:1000533 + Bioworks + + + + + Thermo Finnigan software for data analysis of peptides and proteins. + PSI:MS + + + + + + + + + + + + Micromass software for data acquisition and analysis. + MS + MS:1000534 + MassLynx + + + + + Micromass software for data acquisition and analysis. + PSI:MS + + + + + + + + + + + Bruker software for data analysis. + MS + MS:1000535 + FlexAnalysis + + + + + Bruker software for data analysis. + PSI:MS + + + + + + + + + + + + Applied Biosystems software for data acquisition and analysis. + MS + MS:1000536 + Data Explorer + + + + + Applied Biosystems software for data acquisition and analysis. + PSI:MS + + + + + + + + + + + + Applied Biosystems software for data acquisition and analysis. + MS + MS:1000537 + 4700 Explorer + + + + + Applied Biosystems software for data acquisition and analysis. + PSI:MS + + + + + + + + + A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology. + wolf + MS + MS:1000538 + massWolf + + + + + A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology. + PSI:MS + + + + + + + + + + + + Applied Biosystems MALDI-TOF data acquisition and analysis system. + MS + MS:1000539 + Voyager Biospectrometry Workstation System + + + + + Applied Biosystems MALDI-TOF data acquisition and analysis system. + PSI:MS + + + + + + + + + + Bruker software for data acquisition. + MS + MS:1000540 + FlexControl + + + + + Bruker software for data acquisition. + PSI:MS + + + + + + + + + A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced "readraw". + MS + MS:1000541 + ReAdW + + + + + A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced "readraw". + PSI:MS + + + + + + + + + A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program. + MS + MS:1000542 + MzStar + + + + + A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program. + PSI:MS + + + + + + + + + Data processing attribute used to describe the type of data processing performed on the data file. + MS + MS:1000543 + data processing action + + + + + Data processing attribute used to describe the type of data processing performed on the data file. + PSI:MS + + + + + + + + + Conversion of a file format to Proteomics Standards Initiative mzML file format. + MS + MS:1000544 + Conversion to mzML + + + + + Conversion of a file format to Proteomics Standards Initiative mzML file format. + PSI:MS + + + + + + + + + Conversion of a file format to Institute of Systems Biology mzXML file format. + MS + MS:1000545 + Conversion to mzXML + + + + + Conversion of a file format to Institute of Systems Biology mzXML file format. + PSI:MS + + + + + + + + + Conversion of a file format to Proteomics Standards Initiative mzData file format. + MS + MS:1000546 + Conversion to mzData + + + + + Conversion of a file format to Proteomics Standards Initiative mzData file format. + PSI:MS + + + + + + + + + + + + + + Object Attribute. + MS + MS:1000547 + object attribute + + + + + Object Attribute. + PSI:MS + + + + + + + + + + + + + + + Sample properties that are associated with a value. + MS + MS:1000548 + sample attribute + + + + + Sample properties that are associated with a value. + PSI:MS + + + + + + + + + + + + + + + Selection window properties that are associated with a value. + MS + MS:1000549 + selection window attribute + + + + + Selection window properties that are associated with a value. + PSI:MS + + + + + + + + OBSOLETE Time Unit. + MS + MS:1000550 + This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003). + time unit + true + + + + + OBSOLETE Time Unit. + PSI:MS + + + + + + + + + + + + SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition. + MS + MS:1000551 + Analyst + + + + + SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition. + PSI:MS + + + + + + + + OBSOLETE Maldi Spot Identifier. + MS + MS:1000552 + This former purgatory term was made obsolete. + maldi spot identifier + true + + + + + OBSOLETE Maldi Spot Identifier. + PSI:MS + + + + + + + + + A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology. + MS + MS:1000553 + Trapper + + + + + A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology. + PSI:MS + + + + + + + + + ThermoFinnigan LCQ Deca. + MS + MS:1000554 + LCQ Deca + + + + + ThermoFinnigan LCQ Deca. + PSI:MS + + + + + + + + + LTQ Orbitrap Discovery. + MS + MS:1000555 + LTQ Orbitrap Discovery + + + + + LTQ Orbitrap Discovery. + PSI:MS + + + + + + + + + LTQ Orbitrap XL. + MS + MS:1000556 + LTQ Orbitrap XL + + + + + LTQ Orbitrap XL. + PSI:MS + + + + + + + + + LTQ FT Ultra. + MS + MS:1000557 + LTQ FT Ultra + + + + + LTQ FT Ultra. + PSI:MS + + + + + + + + + GC Quantum. + MS + MS:1000558 + GC Quantum + + + + + GC Quantum. + PSI:MS + + + + + + + + + + + + + + Spectrum type. + MS + MS:1000559 + spectrum type + + + + + Spectrum type. + PSI:MS + + + + + + + + + The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. + MS + MS:1000560 + mass spectrometer file format + + + + + The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. + PSI:MS + + + + + + + + + + + + + + Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data. + MS + MS:1000561 + data file checksum type + + + + + Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data. + PSI:MS + + + + + + + + + Applied Biosystems WIFF file format. + MS + MS:1000562 + ABI WIFF format + + + + + Applied Biosystems WIFF file format. + PSI:MS + + + + + + + + + Thermo Scientific RAW file format. + MS + MS:1000563 + Thermo RAW format + + + + + Thermo Scientific RAW file format. + PSI:MS + + + + + + + + + Proteomics Standards Inititative mzData file format. + MS + MS:1000564 + PSI mzData format + + + + + Proteomics Standards Inititative mzData file format. + PSI:MS + + + + + + + + + Micromass PKL file format. + MS + MS:1000565 + Micromass PKL format + + + + + Micromass PKL file format. + PSI:MS + + + + + + + + + Institute of Systems Biology mzXML file format. + MS + MS:1000566 + ISB mzXML format + + + + + Institute of Systems Biology mzXML file format. + PSI:MS + + + + + + + + + Bruker/Agilent YEP file format. + MS + MS:1000567 + Bruker/Agilent YEP format + + + + + Bruker/Agilent YEP file format. + PSI:MS + + + + + + + + + + + + + + + MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files. + MS + MS:1000568 + MD5 + + + + + MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files. + PSI:MS + + + + + + + + + + + + + + + SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard. + MS + MS:1000569 + SHA-1 + + + + + SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard. + PSI:MS + + + + + + + + + + + + + + Method used to combine the mass spectra. + MS + MS:1000570 + spectra combination + + + + + Method used to combine the mass spectra. + PSI:MS + + + + + + + + + Spectra Sum. + MS + MS:1000571 + sum of spectra + + + + + Spectra Sum. + PSI:MS + + + + + + + + + + + + + + + + + + + + Compression Type. + MS + MS:1000572 + binary data compression type + + + + + Compression Type. + PSI:MS + + + + + + + + + Spectra is combined by calculating the median of the spectra. + MS + MS:1000573 + median of spectra + + + + + Spectra is combined by calculating the median of the spectra. + PSI:MS + + + + + + + + + Zlib. + MS + MS:1000574 + zlib compression + + + + + Zlib. + PSI:MS + + + + + + + + + Spectra is combined by calculating the mean of the spectra. + MS + MS:1000575 + mean of spectra + + + + + Spectra is combined by calculating the mean of the spectra. + PSI:MS + + + + + + + + + No Compression. + MS + MS:1000576 + no compression + + + + + No Compression. + PSI:MS + + + + + + + + + + + + + + + Data file from which an entity is sourced. + source file + MS + MS:1000577 + source data file + + + + + Data file from which an entity is sourced. + PSI:MS + + + + + + + + + LCQ Fleet. + MS + MS:1000578 + LCQ Fleet + + + + + LCQ Fleet. + PSI:MS + + + + + + + + + Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment. + Q1 spectrum + Q3 spectrum + Single-Stage Mass Spectrometry + full spectrum + MS + MS:1000579 + MS1 spectrum + + + + + Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment. + PSI:MS + + + + + + + + + MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n. + multiple-stage mass spectrometry spectrum + nth generation product ion spectrum + product ion spectrum + MS + MS:1000580 + MSn spectrum + + + + + MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n. + PSI:MS + + + + + + + + + Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. + MS + MS:1000581 + CRM spectrum + + + + + Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored. + PSI:MS + + + + + + + + + Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring). + MIM spectrum + multiple ion monitoring spectrum + selected ion monitoring spectrum + MS + MS:1000582 + SIM spectrum + + + + + Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring). + PSI:MS + + + + + + + + + Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space. + MRM spectrum + multiple reaction monitoring spectrum + selected reaction monitoring spectrum + MS + MS:1000583 + SRM spectrum + + + + + Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space. + PSI:MS + + + + + + + + + Proteomics Standards Inititative mzML file format. + MS + MS:1000584 + mzML format + + + + + Proteomics Standards Inititative mzML file format. + PSI:MS + + + + + + + + + + + + + + + Details about a person or organization to contact in case of concern or discussion about the file. + MS + MS:1000585 + contact attribute + + + + + Details about a person or organization to contact in case of concern or discussion about the file. + PSI:MS + + + + + + + + + + + + + + + Name of the contact person or organization. + MS + MS:1000586 + contact name + + + + + Name of the contact person or organization. + PSI:MS + + + + + + + + + + + + + + + Postal address of the contact person or organization. + MS + MS:1000587 + contact address + + + + + Postal address of the contact person or organization. + PSI:MS + + + + + + + + + + + + + + + Uniform Resource Locator related to the contact person or organization. + MS + MS:1000588 + contact URL + + + + + Uniform Resource Locator related to the contact person or organization. + PSI:MS + + + + + + + + + + + + + + + Email address of the contact person or organization. + MS + MS:1000589 + contact email + + + + + Email address of the contact person or organization. + PSI:MS + + + + + + + + + + + + + + + Home institution of the contact person. + MS + MS:1000590 + contact affiliation + + + + + Home institution of the contact person. + PSI:MS + + + + + + + + + A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program. + MS + MS:1000591 + MzWiff + + + + + A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program. + PSI:MS + + + + + + + + + A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process. + MS + MS:1000592 + smoothing + + + + + A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process. + PSI:MS + + + + + + + + + A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values. + MS + MS:1000593 + baseline reduction + + + + + A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values. + PSI:MS + + + + + + + + + The removal of very low intensity data points that are likely to be spurious noise rather than real signal. + thresholding + MS + MS:1000594 + low intensity data point removal + + + + + The removal of very low intensity data points that are likely to be spurious noise rather than real signal. + PSI:MS + + + + + + + + + + + + + + + + + + + + + A data array of relative time offset values from a reference time. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1000595 + time array + + + + + A data array of relative time offset values from a reference time. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + + + + + + An attribute of resolution when recording the detector response in absence of the analyte. + MS + MS:1000596 + measurement method + + + + + An attribute of resolution when recording the detector response in absence of the analyte. + PSI:MS + + + + + + + + + The electrical potential used to impart kinetic energy to ions in a mass spectrometer. + MS + MS:1000597 + ion optics type + + + + + The electrical potential used to impart kinetic energy to ions in a mass spectrometer. + PSI:MS + + + + + + + + + A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions. + ETD + MS + MS:1000598 + electron transfer dissociation + + + + + A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions. + DOI:10.1073/pnas.0402700101 + PMID:15210983 + PSI:MS + + + + + + + + + A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected. + PQD + MS + MS:1000599 + pulsed q dissociation + + + + + A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected. + PSI:MS + + + + + + + + + + Database application and analysis platform for proteomics. + MS + MS:1000600 + Proteios + + + + + Database application and analysis platform for proteomics. + PSI:MS + source:http://www.proteios.org + + + + + + + + + + + Waters software for data analysis. + MS + MS:1000601 + ProteinLynx Global Server + + + + + Waters software for data analysis. + PSI:MS + + + + + + + + + Shimadzu MALDI-TOF instrument model. + MS + MS:1000602 + Shimadzu MALDI-TOF instrument model + + + + + Shimadzu MALDI-TOF instrument model. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments instrument model. + MS + MS:1000603 + Shimadzu Scientific Instruments instrument model + + + + + Shimadzu Scientific Instruments instrument model. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments LCMS-IT-TOF MS. + MS + MS:1000604 + LCMS-IT-TOF + + + + + Shimadzu Scientific Instruments LCMS-IT-TOF MS. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments LCMS-2010EV MS. + MS + MS:1000605 + LCMS-2010EV + + + + + Shimadzu Scientific Instruments LCMS-2010EV MS. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments LCMS-2010A MS. + MS + MS:1000606 + LCMS-2010A + + + + + Shimadzu Scientific Instruments LCMS-2010A MS. + PSI:MS + + + + + + + + + Shimadzu Biotech AXIMA CFR MALDI-TOF MS. + MS + MS:1000607 + AXIMA CFR MALDI-TOF + + + + + Shimadzu Biotech AXIMA CFR MALDI-TOF MS. + PSI:MS + + + + + + + + + Shimadzu Biotech AXIMA-QIT MS. + MS + MS:1000608 + AXIMA-QIT + + + + + Shimadzu Biotech AXIMA-QIT MS. + PSI:MS + + + + + + + + + Shimadzu Biotech AXIMA-CFR plus MS. + MS + MS:1000609 + AXIMA-CFR plus + + + + + Shimadzu Biotech AXIMA-CFR plus MS. + PSI:MS + + + + + + + + + Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS. + MS + MS:1000610 + AXIMA Performance MALDI-TOF/TOF + + + + + Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS. + PSI:MS + + + + + + + + + Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS. + MS + MS:1000611 + AXIMA Confidence MALDI-TOF + + + + + Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS. + PSI:MS + + + + + + + + + Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS. + MS + MS:1000612 + AXIMA Assurance Linear MALDI-TOF + + + + + Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS. + PSI:MS + + + + + + + + + SEQUEST DTA file format. + MS + MS:1000613 + DTA format + + + + + SEQUEST DTA file format. + PSI:MS + + + + + + + + + Peak list file format used by ProteinLynx Global Server. + MS + MS:1000614 + ProteinLynx Global Server mass spectrum XML format + + + + + Peak list file format used by ProteinLynx Global Server. + PSI:MS + + + + + + + + + + ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb. + pwiz + MS + MS:1000615 + ProteoWizard software + + + + + ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb. + PSI:MS + + + + + + + + + + + + + + + A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo "scan event", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time. + MS + MS:1000616 + preset scan configuration + + + + + A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo "scan event", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time. + PSI:MS + + + + + + + + + + + + + + + A data array of electromagnetic radiation wavelength values. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1000617 + wavelength array + + + + + A data array of electromagnetic radiation wavelength values. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + + + + + + + + + + + + + + Highest wavelength observed in an EMR spectrum. + MS + MS:1000618 + highest observed wavelength + + + + + Highest wavelength observed in an EMR spectrum. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + Lowest wavelength observed in an EMR spectrum. + MS + MS:1000619 + lowest observed wavelength + + + + + Lowest wavelength observed in an EMR spectrum. + PSI:MS + + + + + + + + + + OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum). + MS + MS:1000620 + This term was made obsolete because it was replaced by absorption spectrum (MS:1000806). + PDA spectrum + true + + + + + OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum). + PSI:MS + + + + + + + + + An array detector used to record spectra in the ultraviolet and visible region of light. + PDA + MS + MS:1000621 + photodiode array detector + + + + + An array detector used to record spectra in the ultraviolet and visible region of light. + PSI:MS + + + + + + + + + Surveyor PDA. + MS + MS:1000622 + Surveyor PDA + + + + + Surveyor PDA. + PSI:MS + + + + + + + + + Accela PDA. + MS + MS:1000623 + Accela PDA + + + + + Accela PDA. + PSI:MS + + + + + + + + + Inductive detector. + image current detector + MS + MS:1000624 + inductive detector + + + + + Inductive detector. + PSI:MS + + + + + + + + + + + + + + Representation of a chromatographic separation attribute measurement versus time. + MS + MS:1000625 + chromatogram + + + + + Representation of a chromatographic separation attribute measurement versus time. + PSI:MS + + + + + + + + + + + + + + Type of chromatogram measurement being represented. + MS + MS:1000626 + chromatogram type + + + + + Type of chromatogram measurement being represented. + PSI:MS + + + + + + + + + Representation of an array of the measurements of a specific single ion current versus time. + SIC chromatogram + MS + MS:1000627 + selected ion current chromatogram + + + + + Representation of an array of the measurements of a specific single ion current versus time. + PSI:MS + + + + + + + + + Representation of an array of the most intense peaks versus time. + MS + MS:1000628 + basepeak chromatogram + + + + + Representation of an array of the most intense peaks versus time. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Threshold below which some action is taken. + MS + MS:1000629 + low intensity threshold + + + + + Threshold below which some action is taken. + PSI:MS + + + + + + + + + + + + + + Data processing parameter used in the data processing performed on the data file. + MS + MS:1000630 + data processing parameter + + + + + Data processing parameter used in the data processing performed on the data file. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Threshold above which some action is taken. + MS + MS:1000631 + high intensity threshold + + + + + Threshold above which some action is taken. + PSI:MS + + + + + + + + + Waters oa-ToF based Q-Tof Premier. + MS + MS:1000632 + Q-Tof Premier + + + + + Waters oa-ToF based Q-Tof Premier. + PSI:MS + + + + + + + + + + + + + + + A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty. + MS + MS:1000633 + possible charge state + + + + + A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty. + PSI:MS + + + + + + + + + ThermoFinnigan DSQ GC-MS. + MS + MS:1000634 + DSQ + + + + + ThermoFinnigan DSQ GC-MS. + PSI:MS + + + + + + + + + Thermo Scientific ITQ 700 GC-MS. + MS + MS:1000635 + ITQ 700 + + + + + Thermo Scientific ITQ 700 GC-MS. + PSI:MS + + + + + + + + + Thermo Scientific ITQ 900 GC-MS. + MS + MS:1000636 + ITQ 900 + + + + + Thermo Scientific ITQ 900 GC-MS. + PSI:MS + + + + + + + + + Thermo Scientific ITQ 1100 GC-MS. + MS + MS:1000637 + ITQ 1100 + + + + + Thermo Scientific ITQ 1100 GC-MS. + PSI:MS + + + + + + + + + Thermo Scientific LTQ XL MS with ETD. + MS + MS:1000638 + LTQ XL ETD + + + + + Thermo Scientific LTQ XL MS with ETD. + PSI:MS + + + + + + + + + Thermo Scientific LTQ Orbitrap XL MS with ETD. + MS + MS:1000639 + LTQ Orbitrap XL ETD + + + + + Thermo Scientific LTQ Orbitrap XL MS with ETD. + PSI:MS + + + + + + + + + Thermo Scientific DFS HR GC-MS. + MS + MS:1000640 + DFS + + + + + Thermo Scientific DFS HR GC-MS. + PSI:MS + + + + + + + + + Thermo Scientific DSQ II GC-MS. + MS + MS:1000641 + DSQ II + + + + + Thermo Scientific DSQ II GC-MS. + PSI:MS + + + + + + + + + Thermo Scientific MALDI LTQ XL MS. + MS + MS:1000642 + MALDI LTQ XL + + + + + Thermo Scientific MALDI LTQ XL MS. + PSI:MS + + + + + + + + + Thermo Scientific MALDI LTQ Orbitrap MS. + MS + MS:1000643 + MALDI LTQ Orbitrap + + + + + Thermo Scientific MALDI LTQ Orbitrap MS. + PSI:MS + + + + + + + + + Thermo Scientific TSQ Quantum Access MS. + MS + MS:1000644 + TSQ Quantum Access + + + + + Thermo Scientific TSQ Quantum Access MS. + PSI:MS + + + + + + + + + Thermo Scientific Element XR HR-ICP-MS. + MS + MS:1000645 + Element XR + + + + + Thermo Scientific Element XR HR-ICP-MS. + PSI:MS + + + + + + + + + Thermo Scientific Element 2 HR-ICP-MS. + MS + MS:1000646 + Element 2 + + + + + Thermo Scientific Element 2 HR-ICP-MS. + PSI:MS + + + + + + + + + Thermo Scientific Element GD Glow Discharge MS. + MS + MS:1000647 + Element GD + + + + + Thermo Scientific Element GD Glow Discharge MS. + PSI:MS + + + + + + + + + Thermo Scientific GC IsoLink Isotope Ratio MS. + MS + MS:1000648 + GC IsoLink + + + + + Thermo Scientific GC IsoLink Isotope Ratio MS. + PSI:MS + + + + + + + + + Thermo Scientific Exactive MS. + MS + MS:1000649 + Exactive + + + + + Thermo Scientific Exactive MS. + PSI:MS + + + + + + + + + + + Thermo Scientific software for data analysis of peptides and proteins. + MS + MS:1000650 + Proteome Discoverer + + + + + Thermo Scientific software for data analysis of peptides and proteins. + PSI:MS + + + + + + + + + SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200. + MS + MS:1000651 + 3200 QTRAP + + + + + SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200. + PSI:MS + + + + + + + + + SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer. + MS + MS:1000652 + 4800 Plus MALDI TOF/TOF + + + + + SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer. + PSI:MS + + + + + + + + + SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS. + MS + MS:1000653 + API 3200 + + + + + SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS. + PSI:MS + + + + + + + + + SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS. + MS + MS:1000654 + API 5000 + + + + + SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS. + PSI:MS + + + + + + + + + SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite. + MS + MS:1000655 + QSTAR Elite + + + + + SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite. + PSI:MS + + + + + + + + + Applied Biosystems|MDS SCIEX QSTAR Pulsar. + MS + MS:1000656 + QSTAR Pulsar + + + + + Applied Biosystems|MDS SCIEX QSTAR Pulsar. + PSI:MS + + + + + + + + + Applied Biosystems|MDS SCIEX QSTAR XL. + MS + MS:1000657 + QSTAR XL + + + + + Applied Biosystems|MDS SCIEX QSTAR XL. + PSI:MS + + + + + + + + + Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer. + MS + MS:1000658 + 4800 Proteomics Analyzer + + + + + Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer. + PSI:MS + + + + + + + + + + + + SCIEX or Applied Biosystems software for data acquisition and analysis. + MS + MS:1000659 + 4000 Series Explorer Software + + + + + SCIEX or Applied Biosystems software for data acquisition and analysis. + PSI:MS + + + + + + + + + + + + SCIEX or Applied Biosystems software for data acquisition and analysis. + MS + MS:1000661 + GPS Explorer + + + + + SCIEX or Applied Biosystems software for data acquisition and analysis. + PSI:MS + + + + + + + + + + + SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification. + MS + MS:1000662 + LightSight Software + + + + + SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification. + PSI:MS + + + + + + + + + + + SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant. + MS + MS:1000663 + ProteinPilot Software + + + + + SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for tissue imaging. + MS + MS:1000664 + TissueView Software + + + + + Applied Biosystems|MDS SCIEX software for tissue imaging. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling. + MS + MS:1000665 + MarkerView Software + + + + + Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for MRM assay development. + MS + MS:1000666 + MRMPilot Software + + + + + Applied Biosystems|MDS SCIEX software for MRM assay development. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for bio-related data exploration. + MS + MS:1000667 + BioAnalyst + + + + + Applied Biosystems|MDS SCIEX software for bio-related data exploration. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for protein identification. + MS + MS:1000668 + Pro ID + + + + + Applied Biosystems|MDS SCIEX software for protein identification. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT. + MS + MS:1000669 + Pro ICAT + + + + + Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ. + MS + MS:1000670 + Pro Quant + + + + + Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for MS-BLAST identification. + MS + MS:1000671 + Pro BLAST + + + + + Applied Biosystems|MDS SCIEX software for MS-BLAST identification. + PSI:MS + + + + + + + + + SCIEX Cliquid software for data analysis and quantitation. + MS + MS:1000672 + Cliquid + + + + + SCIEX Cliquid software for data analysis and quantitation. + PSI:MS + + + + + + + + + Applied Biosystems|MDS SCIEX software for MRM assay development. + MS + MS:1000673 + MIDAS Workflow Designer + + + + + Applied Biosystems|MDS SCIEX software for MRM assay development. + PSI:MS + + + + + + + + + + + Applied Biosystems|MDS SCIEX software for MRM-based quantitation. + MS + MS:1000674 + MultiQuant + + + + + Applied Biosystems|MDS SCIEX software for MRM-based quantitation. + PSI:MS + + + + + + + + + The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. + MS + MS:1000675 + 6220 Time-of-Flight LC/MS + + + + + The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. + PSI:MS + + + + + + + + + The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. + MS + MS:1000676 + 6510 Quadrupole Time-of-Flight LC/MS + + + + + The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. + PSI:MS + + + + + + + + + The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. + MS + MS:1000677 + 6520A Quadrupole Time-of-Flight LC/MS + + + + + The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources. + PSI:MS + + + + + + + + + + Software for data acquisition of 6000 series instruments. + MS + MS:1000678 + MassHunter Data Acquisition + + + + + Software for data acquisition of 6000 series instruments. + PSI:MS + + + + + + + + + + Software for open access data acquisition. + MS + MS:1000679 + MassHunter Easy Access + + + + + Software for open access data acquisition. + PSI:MS + + + + + + + + + + + Software for data analysis of data from 6000 series instruments. + MS + MS:1000680 + MassHunter Qualitative Analysis + + + + + Software for data analysis of data from 6000 series instruments. + PSI:MS + + + + + + + + + + + Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data. + MS + MS:1000681 + MassHunter Quantitative Analysis + + + + + Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data. + PSI:MS + + + + + + + + + + + Software for identification of metabolites. + MS + MS:1000682 + MassHunter Metabolite ID + + + + + Software for identification of metabolites. + PSI:MS + + + + + + + + + + + Software for protein characterization. + MS + MS:1000683 + MassHunter BioConfirm + + + + + Software for protein characterization. + PSI:MS + + + + + + + + + + + Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. + MS + MS:1000684 + Genespring MS + + + + + Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. + PSI:MS + + + + + + + + + + + Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. + MS + MS:1000685 + MassHunter Mass Profiler + + + + + Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data. + PSI:MS + + + + + + + + + + + Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites. + MS + MS:1000686 + METLIN + + + + + Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites. + PSI:MS + + + + + + + + + + + Software for protein identification and characterization of complex protein digest mixtures. + MS + MS:1000687 + Spectrum Mill for MassHunter Workstation + + + + + Software for protein identification and characterization of complex protein digest mixtures. + PSI:MS + + + + + + + + + + + + Software for data analysis of 6300 series ion trap mass spectrometers. + MS + MS:1000688 + 6300 Series Ion Trap Data Analysis Software + + + + + Software for data analysis of 6300 series ion trap mass spectrometers. + PSI:MS + + + + + + + + + Agilent software for data acquisition and analysis. + MS + MS:1000689 + Agilent software + + + + + Agilent software for data acquisition and analysis. + PSI:MS + + + + + + + + + SCIEX or Applied Biosystems software for data acquisition and analysis. + MS + MS:1000690 + SCIEX software + + + + + SCIEX or Applied Biosystems software for data acquisition and analysis. + PSI:MS + + + + + + + + + Applied Biosystems|MDS SCIEX software for data acquisition and analysis. + MS + MS:1000691 + Applied Biosystems software + + + + + Applied Biosystems|MDS SCIEX software for data acquisition and analysis. + PSI:MS + + + + + + + + + Bruker software for data acquisition and analysis. + MS + MS:1000692 + Bruker software + + + + + Bruker software for data acquisition and analysis. + PSI:MS + + + + + + + + + Thermo Finnigan software for data acquisition and analysis. + MS + Bioworks Browser + MS:1000693 + Thermo Finnigan software + + + + + Thermo Finnigan software for data acquisition and analysis. + PSI:MS + + + + + + + + + Waters software for data acquisition and analysis. + MS + MS:1000694 + Waters software + + + + + Waters software for data acquisition and analysis. + PSI:MS + + + + + + + + + Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. + MS + MS:1000695 + apex ultra + + + + + Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR. + PSI:MS + + + + + + + + + Bruker Daltonics' autoflex III smartbeam: MALDI TOF. + MS + MS:1000696 + autoflex III smartbeam + + + + + Bruker Daltonics' autoflex III smartbeam: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' HCT Series. + MS + MS:1000697 + Bruker Daltonics HCT Series + + + + + Bruker Daltonics' HCT Series. + PSI:MS + + + + + + + + + Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI. + MS + MS:1000698 + HCTultra + + + + + Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR. + MS + MS:1000699 + HCTultra PTM + + + + + Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR. + PSI:MS + + + + + + + + + Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD. + MS + MS:1000700 + HCTultra ETD II + + + + + Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD. + PSI:MS + + + + + + + + + Bruker Daltonics' microflex LT: MALDI TOF. + MS + MS:1000701 + microflex LT + + + + + Bruker Daltonics' microflex LT: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI. + MS + MS:1000702 + micrOTOF + + + + + Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI. + PSI:MS + + + + + + + + + Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI. + MS + MS:1000703 + micrOTOF-Q + + + + + Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI. + MS + MS:1000704 + micrOTOF-Q II + + + + + Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF. + MS + MS:1000705 + ultraflex III TOF/TOF + + + + + Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF. + PSI:MS + + + + + + + + + + Bruker software for data acquisition. + MS + MS:1000706 + apexControl + + + + + Bruker software for data acquisition. + PSI:MS + + + + + + + + + + + Bruker software for data analysis. + MS + MS:1000707 + BioTools + + + + + Bruker software for data analysis. + PSI:MS + + + + + + + + + + + Bruker CLINPROT software. + MS + MS:1000708 + CLINPROT + + + + + Bruker CLINPROT software. + PSI:MS + + + + + + + + + + + Bruker CLINPROT micro software. + MS + MS:1000709 + CLINPROT micro + + + + + Bruker CLINPROT micro software. + PSI:MS + + + + + + + + + Bruker CLINPROT robot software. + MS + MS:1000710 + CLINPROT robot + + + + + Bruker CLINPROT robot software. + PSI:MS + + + + + + + + + Bruker ClinProTools software. + MS + MS:1000711 + ClinProTools + + + + + Bruker ClinProTools software. + PSI:MS + + + + + + + + + + + Bruker Compass software. + MS + MS:1000712 + Compass + + + + + Bruker Compass software. + PSI:MS + + + + + + + + + + + Bruker Compass for HCT/esquire software. + MS + MS:1000713 + Compass for HCT/esquire + + + + + Bruker Compass for HCT/esquire software. + PSI:MS + + + + + + + + + + + Bruker Compass for micrOTOF software. + MS + MS:1000714 + Compass for micrOTOF + + + + + Bruker Compass for micrOTOF software. + PSI:MS + + + + + + + + + + + Bruker compass OpenAccess software. + MS + MS:1000715 + Compass OpenAccess + + + + + Bruker compass OpenAccess software. + PSI:MS + + + + + + + + + Bruker compass Security Pack software. + MS + MS:1000716 + Compass Security Pack + + + + + Bruker compass Security Pack software. + PSI:MS + + + + + + + + + + Bruker stand-alone software for data conversion. + MS + MS:1000717 + CompassXport + + + + + Bruker stand-alone software for data conversion. + PSI:MS + + + + + + + + + + Bruker software library for data access. + MS + MS:1000718 + CompassXtract + + + + + Bruker software library for data access. + PSI:MS + + + + + + + + + + + Bruker software for data analysis. + MS + MS:1000719 + DataAnalysis + + + + + Bruker software for data analysis. + PSI:MS + + + + + + + + + + Bruker software for data acquisition. + MS + MS:1000720 + dpControl + + + + + Bruker software for data acquisition. + PSI:MS + + + + + + + + + + Bruker software for data acquisition. + MS + MS:1000721 + esquireControl + + + + + Bruker software for data acquisition. + PSI:MS + + + + + + + + + + + Bruker software for data analysis. + MS + MS:1000722 + flexImaging + + + + + Bruker software for data analysis. + PSI:MS + + + + + + + + + Bruker GENOLINK software. + MS + MS:1000723 + GENOLINK + + + + + Bruker GENOLINK software. + PSI:MS + + + + + + + + + Bruker GenoTools software. + MS + MS:1000724 + GenoTools + + + + + Bruker GenoTools software. + PSI:MS + + + + + + + + + + Bruker software for data acquisition. + MS + MS:1000725 + HCTcontrol + + + + + Bruker software for data acquisition. + PSI:MS + + + + + + + + + + Bruker software for data acquisition. + MS + MS:1000726 + micrOTOFcontrol + + + + + Bruker software for data acquisition. + PSI:MS + + + + + + + + + Bruker PolyTools software. + MS + MS:1000727 + PolyTools + + + + + Bruker PolyTools software. + PSI:MS + + + + + + + + + + + Bruker software for data analysis. + MS + MS:1000728 + ProfileAnalysis + + + + + Bruker software for data analysis. + PSI:MS + + + + + + + + + Bruker PROTEINEER software. + MS + MS:1000729 + PROTEINEER + + + + + Bruker PROTEINEER software. + PSI:PI + + + + + + + + + Bruker PROTEINEER dp software. + MS + MS:1000730 + PROTEINEER dp + + + + + Bruker PROTEINEER dp software. + PSI:PI + + + + + + + + + Bruker PROTEINEER fc software. + MS + MS:1000731 + PROTEINEER fc + + + + + Bruker PROTEINEER fc software. + PSI:PI + + + + + + + + + Bruker PROTEINEER spII software. + MS + MS:1000732 + PROTEINEER spII + + + + + Bruker PROTEINEER spII software. + PSI:PI + + + + + + + + + Bruker PROTEINEER-LC software. + MS + MS:1000733 + PROTEINEER-LC + + + + + Bruker PROTEINEER-LC software. + PSI:PI + + + + + + + + + + Bruker ProteinScape software. + MS + MS:1000734 + ProteinScape + + + + + Bruker ProteinScape software. + PSI:PI + + + + + + + + + BrukerPureDisk software. + MS + MS:1000735 + PureDisk + + + + + BrukerPureDisk software. + PSI:MS + + + + + + + + + + + Bruker software for data analysis. + MS + MS:1000736 + QuantAnalysis + + + + + Bruker software for data analysis. + PSI:MS + + + + + + + + + + Bruker software for data acquisition. + MS + MS:1000737 + spControl + + + + + Bruker software for data acquisition. + PSI:MS + + + + + + + + + Bruker TargetAnalysis software. + MS + MS:1000738 + TargetAnalysis + + + + + Bruker TargetAnalysis software. + PSI:MS + + + + + + + + + + Bruker WARP-LC software. + MS + MS:1000739 + WARP-LC + + + + + Bruker WARP-LC software. + PSI:MS + + + + + + + + + Parameter file used to configure the acquisition of raw data on the instrument. + MS + MS:1000740 + parameter file + + + + + Parameter file used to configure the acquisition of raw data on the instrument. + PSI:MS + + + + + + + + + Conversion to dta format. + MS + MS:1000741 + Conversion to dta + + + + + Conversion to dta format. + PSI:MS + + + + + + + + + + Thermo Finnigan SRF file format. + MS + MS:1000742 + Bioworks SRF format + + + + + Thermo Finnigan SRF file format. + PSI:MS + + + + + + + + + Thermo Scientific TSQ Quantum Ultra AM. + MS + MS:1000743 + TSQ Quantum Ultra AM + + + + + Thermo Scientific TSQ Quantum Ultra AM. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Mass-to-charge ratio of an selected ion. + MS + MS:1000744 + selected ion m/z + + + + + Mass-to-charge ratio of an selected ion. + PSI:MS + + + + + + + + + The correction of the spectrum scan times, as used e.g. in label-free proteomics. + MS + MS:1000745 + retention time alignment + + + + + The correction of the spectrum scan times, as used e.g. in label-free proteomics. + PSI:MS + + + + + + + + + The removal of very high intensity data points. + MS + MS:1000746 + high intensity data point removal + + + + + The removal of very high intensity data points. + PSI:MS + + + + + + + + + + + + + + + The time that a data processing action was finished. + MS + MS:1000747 + completion time + + + + + The time that a data processing action was finished. + PSI:MS + + + + + + + + + ThermoFinnigan SSQ 7000 MS. + MS + MS:1000748 + SSQ 7000 + + + + + ThermoFinnigan SSQ 7000 MS. + PSI:MS + + + + + + + + + ThermoFinnigan TSQ 7000 MS. + MS + MS:1000749 + TSQ 7000 + + + + + ThermoFinnigan TSQ 7000 MS. + PSI:MS + + + + + + + + + ThermoFinnigan TSQ MS. + MS + MS:1000750 + TSQ + + + + + ThermoFinnigan TSQ MS. + PSI:MS + + + + + + + + + Thermo Scientific TSQ Quantum Ultra. + MS + MS:1000751 + TSQ Quantum Ultra + + + + + Thermo Scientific TSQ Quantum Ultra. + PSI:MS + + + + + + + + + + TOPP (The OpenMS proteomics pipeline) software. + MS + MS:1000752 + TOPP software + + + + + TOPP (The OpenMS proteomics pipeline) software. + PSI:MS + + + + + + + + + Removes the baseline from profile spectra using a top-hat filter. + MS + MS:1000753 + BaselineFilter + + + + + Removes the baseline from profile spectra using a top-hat filter. + PSI:MS + + + + + + + + + Exports data from an OpenMS database to a file. + MS + MS:1000754 + DBExporter + + + + + Exports data from an OpenMS database to a file. + PSI:MS + + + + + + + + + Imports data to an OpenMS database. + MS + MS:1000755 + DBImporter + + + + + Imports data to an OpenMS database. + PSI:MS + + + + + + + + + Converts between different MS file formats. + MS + MS:1000756 + FileConverter + + + + + Converts between different MS file formats. + PSI:MS + + + + + + + + + Extracts or manipulates portions of data from peak, feature or consensus feature files. + MS + MS:1000757 + FileFilter + + + + + Extracts or manipulates portions of data from peak, feature or consensus feature files. + PSI:MS + + + + + + + + + Merges several MS files into one file. + MS + MS:1000758 + FileMerger + + + + + Merges several MS files into one file. + PSI:MS + + + + + + + + + Applies an internal calibration. + MS + MS:1000759 + InternalCalibration + + + + + Applies an internal calibration. + PSI:MS + + + + + + + + + OBSOLETE Corrects retention time distortions between maps. + MS + MS:1000760 + This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch. + MapAligner + true + + + + + OBSOLETE Corrects retention time distortions between maps. + PSI:MS + + + + + + + + + Normalizes peak intensities in an MS run. + MS + MS:1000761 + MapNormalizer + + + + + Normalizes peak intensities in an MS run. + PSI:MS + + + + + + + + + OBSOLETE Removes noise from profile spectra by using different smoothing techniques. + MS + MS:1000762 + This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch. + NoiseFilter + true + + + + + OBSOLETE Removes noise from profile spectra by using different smoothing techniques. + PSI:MS + + + + + + + + + OBSOLETE Finds mass spectrometric peaks in profile mass spectra. + MS + MS:1000763 + This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch. + PeakPicker + true + + + + + OBSOLETE Finds mass spectrometric peaks in profile mass spectra. + PSI:MS + + + + + + + + + Transforms an LC/MS map into a resampled map or a png image. + MS + MS:1000764 + Resampler + + + + + Transforms an LC/MS map into a resampled map or a png image. + PSI:MS + + + + + + + + + OBSOLETE Applies a filter to peak spectra. + MS + MS:1000765 + This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch. + SpectraFilter + true + + + + + OBSOLETE Applies a filter to peak spectra. + PSI:MS + + + + + + + + + Applies time of flight calibration. + MS + MS:1000766 + TOFCalibration + + + + + Applies time of flight calibration. + PSI:MS + + + + + + + + + + + + + + Describes how the native spectrum identifiers are formated. + nativeID format + MS + MS:1000767 + native spectrum identifier format + + + + + Describes how the native spectrum identifiers are formated. + PSI:MS + + + + + + + + + Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger. + MS + MS:1000768 + Thermo nativeID format + + + + + Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger. + PSI:MS + + + + + + + + + Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. + MS + MS:1000769 + Waters nativeID format + + + + + Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger. + MS + MS:1000770 + WIFF nativeID format + + + + + Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Native format defined by scan=xsd:nonNegativeInteger. + MS + MS:1000771 + Bruker/Agilent YEP nativeID format + + + + + Native format defined by scan=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Native format defined by scan=xsd:nonNegativeInteger. + MS + MS:1000772 + Bruker BAF nativeID format + + + + + Native format defined by scan=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Native format defined by file=xsd:IDREF. + MS + MS:1000773 + The nativeID must be the same as the source file ID. + Bruker FID nativeID format + + + + + Native format defined by file=xsd:IDREF. + PSI:MS + + + + + + + + + Native format defined by index=xsd:nonNegativeInteger. + MS + MS:1000774 + Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. + multiple peak list nativeID format + + + + + Native format defined by index=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Native format defined by file=xsd:IDREF. + MS + MS:1000775 + The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. + single peak list nativeID format + + + + + Native format defined by file=xsd:IDREF. + PSI:MS + + + + + + + + + Native format defined by scan=xsd:nonNegativeInteger. + MS + MS:1000776 + Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. + scan number only nativeID format + + + + + Native format defined by scan=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Native format defined by spectrum=xsd:nonNegativeInteger. + MS + MS:1000777 + Used for conversion from mzData. The spectrum id attribute is referenced. + spectrum identifier nativeID format + + + + + Native format defined by spectrum=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm. + MS + MS:1000778 + charge state calculation + + + + + A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm. + PSI:MS + + + + + + + + + Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z. + MS + MS:1000779 + below precursor intensity dominance charge state calculation + + + + + Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z. + PSI:MS + + + + + + + + + A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions. + MS + MS:1000780 + precursor recalculation + + + + + A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions. + PSI:MS + + + + + + + + + Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans. + MS + MS:1000781 + msPrefix precursor recalculation + + + + + Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans. + PSI:MS + + + + + + + + + Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques. + MS + MS:1000782 + Savitzky-Golay smoothing + + + + + Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques. + PSI:MS + + + + + + + + + Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible. + MS + MS:1000783 + LOWESS smoothing + + + + + Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible. + PSI:MS + + + + + + + + + Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function. + Weierstrass transform + binomial smoothing + MS + MS:1000784 + Gaussian smoothing + + + + + Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function. + PSI:MS + + + + + + + + + Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect. + box smoothing + boxcar smoothing + sliding average smoothing + MS + MS:1000785 + moving average smoothing + + + + + Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect. + PSI:MS + + + + + + + + + + + + + + + A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added. + binary-data-type:MS:1000519 + binary-data-type:MS:1000521 + binary-data-type:MS:1000522 + binary-data-type:MS:1000523 + binary-data-type:MS:1001479 + MS + MS:1000786 + non-standard data array + + + + + A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added. + PSI:MS + + + + + binary-data-type:MS:1000519 + 32-bit integer + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000522 + 64-bit integer + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + binary-data-type:MS:1001479 + null-terminated ASCII string + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Threshold at or below which some action is taken. + MS + MS:1000787 + inclusive low intensity threshold + + + + + Threshold at or below which some action is taken. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Threshold at or above which some action is taken. + MS + MS:1000788 + inclusive high intensity threshold + + + + + Threshold at or above which some action is taken. + PSI:MS + + + + + + + + + MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions. + MS + MS:1000789 + enhanced multiply charged spectrum + + + + + MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions. + PSI:MS + + + + + + + + + MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation. + MS + MS:1000790 + time-delayed fragmentation spectrum + + + + + MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation. + PSI:MS + + + + + + + + OBSOLETE Scan with enhanced resolution. + MS + MS:1000791 + This term was made obsolete because it was merged with zoom scan (MS:1000497). + enhanced resolution scan + true + + + + + OBSOLETE Scan with enhanced resolution. + PSI:MS + + + + + + + + + + + + + + + Isolation window parameter. + MS + MS:1000792 + isolation window attribute + + + + + Isolation window parameter. + PSI:MS + + + + + + + + + + + + + + + + + + + + + OBSOLETE The highest m/z being isolated in an isolation window. + MS + MS:1000793 + This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. + isolation window upper limit + true + + + + + OBSOLETE The highest m/z being isolated in an isolation window. + PSI:MS + + + + + + + + + + + + + + + + + + + + + OBSOLETE The lowest m/z being isolated in an isolation window. + MS + MS:1000794 + This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. + isolation window lower limit + true + + + + + OBSOLETE The lowest m/z being isolated in an isolation window. + PSI:MS + + + + + + + + + Use this term if only one scan was recorded or there is no information about scans available. + MS + MS:1000795 + no combination + + + + + Use this term if only one scan was recorded or there is no information about scans available. + PSI:MS + + + + + + + + + + + + + + + + Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file. + MS + MS:1000796 + This is the preferred storage place for the spectrum TITLE from an MGF peak list. + spectrum title + + + + + Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file. + PSI:MS + + + + + + + + + + + + + + + + A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. + MS + MS:1000797 + This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list. + peak list scans + + + + + A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. + PSI:MS + + + + + + + + + + + + + + + + A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. + MS + MS:1000798 + This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list. + peak list raw scans + + + + + A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term. + PSI:MS + + + + + + + + + + + + + + + A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added. + MS + MS:1000799 + custom unreleased software tool + + + + + A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added. + PSI:MS + + + + + + + + + + + + + + + The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported. + MS + MS:1000800 + mass resolving power + + + + + The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported. + PSI:MS + + + + + + + + + Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported. + sum peak picking + MS + MS:1000801 + area peak picking + + + + + Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported. + PSI:MS + + + + + + + + + Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported. + max peak picking + MS + MS:1000802 + height peak picking + + + + + Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value. + MS + MS:1000803 + analyzer scan offset + + + + + Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value. + PSI:MS + + + + + + + + + + A plot of the relative intensity of electromagnetic radiation as a function of the wavelength. + EMR spectrum + MS + MS:1000804 + electromagnetic radiation spectrum + + + + + A plot of the relative intensity of electromagnetic radiation as a function of the wavelength. + PSI:MS + + + + + + + + + + A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited. + MS + MS:1000805 + emission spectrum + + + + + A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited. + PSI:MS + + + + + + + + + + A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited. + MS + MS:1000806 + absorption spectrum + + + + + A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited. + PSI:MS + + + + + + + + + Unit describing the scan rate of a spectrum in Thomson per second. + MS + MS:1000807 + Th/s + + + + + Unit describing the scan rate of a spectrum in Thomson per second. + PSI:MS + + + + + + + + + + + + + + + Chromatogram properties that are associated with a value. + MS + MS:1000808 + chromatogram attribute + + + + + Chromatogram properties that are associated with a value. + PSI:MS + + + + + + + + + + + + + + + A free-form text title describing a chromatogram. + MS + MS:1000809 + This is the preferred storage place for the spectrum title. + chromatogram title + + + + + A free-form text title describing a chromatogram. + PSI:MS + + + + + + + + + + Representation of the current of ions versus time. + MS + MS:1000810 + ion current chromatogram + + + + + Representation of the current of ions versus time. + PSI:MS + + + + + + + + + + Representation of electromagnetic properties versus time. + EMR radiation chromatogram + MS + MS:1000811 + electromagnetic radiation chromatogram + + + + + Representation of electromagnetic properties versus time. + PSI:MS + + + + + + + + + Representation of light absorbed by the sample versus time. + MS + MS:1000812 + absorption chromatogram + + + + + Representation of light absorbed by the sample versus time. + PSI:MS + + + + + + + + + Representation of light emitted by the sample versus time. + MS + MS:1000813 + emission chromatogram + + + + + Representation of light emitted by the sample versus time. + PSI:MS + + + + + + + + + The number of counted events observed per second in one or a group of elements of a detector. + MS + MS:1000814 + counts per second + + + + + The number of counted events observed per second in one or a group of elements of a detector. + PSI:MS + + + + + + + + + Bruker BAF raw file format. + MS + MS:1000815 + Bruker BAF format + + + + + Bruker BAF raw file format. + PSI:MS + + + + + + + + + Bruker HyStar U2 file format. + MS + MS:1000816 + Bruker U2 format + + + + + Bruker HyStar U2 file format. + PSI:MS + + + + + + + + + Bruker software for hyphenated experiments. + MS + MS:1000817 + HyStar + + + + + Bruker software for hyphenated experiments. + PSI:MS + + + + + + + + + + Acquity UPLC Photodiode Array Detector. + MS + MS:1000818 + Acquity UPLC PDA + + + + + Acquity UPLC Photodiode Array Detector. + PSI:MS + + + + + + + + + + Acquity UPLC Fluorescence Detector. + MS + MS:1000819 + Acquity UPLC FLR + + + + + Acquity UPLC Fluorescence Detector. + PSI:MS + + + + + + + + + + + + + + + A data array of flow rate measurements. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1000820 + flow rate array + + + + + A data array of flow rate measurements. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + + + + + + + A data array of pressure measurements. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1000821 + pressure array + + + + + A data array of pressure measurements. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + + + + + + + A data array of temperature measurements. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1000822 + temperature array + + + + + A data array of temperature measurements. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. + MS + MS:1000823 + Bruker U2 nativeID format + + + + + Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format. + MS + MS:1000824 + no nativeID format + + + + + No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format. + PSI:MS + + + + + + + + + Bruker FID file format. + MS + MS:1000825 + Bruker FID format + + + + + Bruker FID file format. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography. + MS + MS:1000826 + elution time + + + + + The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The primary or reference m/z about which the isolation window is defined. + MS + MS:1000827 + isolation window target m/z + + + + + The primary or reference m/z about which the isolation window is defined. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. + MS + MS:1000828 + isolation window lower offset + + + + + The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. + MS + MS:1000829 + isolation window upper offset + + + + + The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. + PSI:MS + + + + + + + + + + + + + + + Properties of the preparation steps which took place before the measurement was performed. + MS + MS:1000831 + sample preparation + + + + + Properties of the preparation steps which took place before the measurement was performed. + PSI:MS + + + + + + + + + + + + + + Attributes to describe the technique how the sample is prepared with the matrix solution. + MS + MS:1000832 + MALDI matrix application + + + + + Attributes to describe the technique how the sample is prepared with the matrix solution. + PSI:MS + + + + + + + + + + + + + + Describes the technique how the matrix is put on the sample target. + MS + MS:1000833 + matrix application type + + + + + Describes the technique how the matrix is put on the sample target. + PSI:MS + + + + + + + + + + + + + + + Describes the chemical solution used as matrix. + MS + MS:1000834 + matrix solution + + + + + Describes the chemical solution used as matrix. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Concentration of the chemical solution used as matrix. + MS + MS:1000835 + matrix solution concentration + + + + + Concentration of the chemical solution used as matrix. + PSI:MS + + + + + + + + + Dried droplet in MALDI matrix preparation. + MS + MS:1000836 + dried droplet MALDI matrix preparation + + + + + Dried droplet in MALDI matrix preparation. + PSI:MS + + + + + + + + + Printed MALDI matrix preparation. + MS + MS:1000837 + printed MALDI matrix preparation + + + + + Printed MALDI matrix preparation. + PSI:MS + + + + + + + + + Sprayed MALDI matrix preparation. + MS + MS:1000838 + sprayed MALDI matrix preparation + + + + + Sprayed MALDI matrix preparation. + PSI:MS + + + + + + + + + + Precoated MALDI sample plate. + MS + MS:1000839 + precoated MALDI sample plate + + + + + Precoated MALDI sample plate. + PSI:MS + + + + + + + + + + + + + + Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation. + MS + MS:1000840 + laser + + + + + Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation. + PSI:MS + + + + + + + + + + + + + + Laser properties that are associated with a value. + MS + MS:1000841 + laser attribute + + + + + Laser properties that are associated with a value. + PSI:MS + + + + + + + + + + + + + + Type of laser used for desorption purpose. + MS + MS:1000842 + laser type + + + + + Type of laser used for desorption purpose. + PSI:MS + + + + + + + + + + + + + + + + + + + + + OBSOLETE The distance between two peaks of the emitted laser beam. + MS + MS:1000843 + This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242). + wavelength + true + + + + + OBSOLETE The distance between two peaks of the emitted laser beam. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Describes the diameter of the laser beam in x direction. + MS + MS:1000844 + focus diameter x + + + + + Describes the diameter of the laser beam in x direction. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Describes the diameter of the laser beam in y direction. + MS + MS:1000845 + focus diameter y + + + + + Describes the diameter of the laser beam in y direction. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Describes output energy of the laser system. May be attenuated by filters or other means. + MS + MS:1000846 + pulse energy + + + + + Describes output energy of the laser system. May be attenuated by filters or other means. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Describes how long the laser beam was emitted from the laser device. + MS + MS:1000847 + pulse duration + + + + + Describes how long the laser beam was emitted from the laser device. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Describes the reduction of the intensity of the laser beam energy. + MS + MS:1000848 + attenuation + + + + + Describes the reduction of the intensity of the laser beam energy. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Describes the angle between the laser beam and the sample target. + MS + MS:1000849 + impact angle + + + + + Describes the angle between the laser beam and the sample target. + PSI:MS + + + + + + + + + Laser which is powered by a gaseous medium. + MS + MS:1000850 + gas laser + + + + + Laser which is powered by a gaseous medium. + PSI:MS + + + + + + + + + Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states. + MS + MS:1000851 + solid-state laser + + + + + Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states. + PSI:MS + + + + + + + + + Dye lasers use an organic dye as the gain medium. + MS + MS:1000852 + dye-laser + + + + + Dye lasers use an organic dye as the gain medium. + PSI:MS + + + + + + + + + Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term. + MS + MS:1000853 + free electron laser + + + + + Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term. + PSI:MS + + + + + + + + + Thermo Scientific LTQ XL MS. + MS + MS:1000854 + LTQ XL + + + + + Thermo Scientific LTQ XL MS. + PSI:MS + + + + + + + + + Thermo Scientific LTQ Velos MS. + MS + MS:1000855 + LTQ Velos + + + + + Thermo Scientific LTQ Velos MS. + PSI:MS + + + + + + + + + Thermo Scientific LTQ Velos MS with ETD. + MS + MS:1000856 + LTQ Velos ETD + + + + + Thermo Scientific LTQ Velos MS with ETD. + PSI:MS + + + + + + + + + Properties of the described run. + MS + MS:1000857 + run attribute + + + + + Properties of the described run. + PSI:MS + + + + + + + + + + + + + + + Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information. + MS + MS:1000858 + fraction identifier + + + + + Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information. + PSI:MS + + + + + + + + + Group of two or more atoms held together by chemical bonds. + MS + MS:1000859 + molecule + + + + + Group of two or more atoms held together by chemical bonds. + https://en.wikipedia.org/wiki/Molecule + + + + + + + + + A molecule of low molecular weight that is composed of two or more amino acid residues. + MS + MS:1000860 + peptide + + + + + A molecule of low molecular weight that is composed of two or more amino acid residues. + PSI:MS + + + + + + + + + + + + + + A physical characteristic of a molecular entity. + MS + MS:1000861 + molecular entity property + + + + + A physical characteristic of a molecular entity. + PSI:MS + + + + + + + + + + + + + + + The pH of a solution at which a charged molecule does not migrate in an electric field. + pI + MS + MS:1000862 + isoelectric point + + + + + The pH of a solution at which a charged molecule does not migrate in an electric field. + PSI:MS + + + + + + + + + + + + + + + The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm. + predicted pI + MS + MS:1000863 + predicted isoelectric point + + + + + The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm. + PSI:MS + + + + + + + + + A combination of symbols used to express the chemical composition of a molecule. + MS + MS:1000864 + chemical formula + + + + + A combination of symbols used to express the chemical composition of a molecule. + EDAM:0846 + + + + + + + + + + + + + + + A chemical formula which expresses the proportions of the elements present in a substance. + MS + MS:1000865 + empirical formula + + + + + A chemical formula which expresses the proportions of the elements present in a substance. + PSI:MS + + + + + + + + + + + + + + + A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked. + MS + MS:1000866 + molecular formula + + + + + A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked. + PSI:MS + + + + + + + + + + + + + + + A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other. + MS + MS:1000867 + structural formula + + + + + A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other. + PSI:MS + + + + + + + + + + + + + + + The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. + MS + MS:1000868 + SMILES formula + + + + + The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. + EDAM:2301 + + + + + + + + + + + + + + + + + + + + + The gas pressure of the collision gas used for collisional excitation. + MS + MS:1000869 + collision gas pressure + + + + + The gas pressure of the collision gas used for collisional excitation. + PSI:MS + + + + + + + + + OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000. + MS + MS:1000870 + This term was obsoleted because was redundant to MS:1000139. + 4000 QTRAP + true + + + + + OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000. + PSI:MS + + + + + + + + + Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs. + MS + MS:1000871 + SRM software + + + + + Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs. + PSI:MS + + + + + + + + + Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. + MS + MS:1000872 + MaRiMba + + + + + Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. + http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba + + + + + + + + + Software used to predict or calculate numerical attributes of peptides. + MS + MS:1000873 + peptide attribute calculation software + + + + + Software used to predict or calculate numerical attributes of peptides. + PSI:MS + + + + + + + + + Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence. + MS + MS:1000874 + SSRCalc + + + + + Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence. + http://hs2.proteome.ca/SSRCalc/SSRCalc.html + + + + + + + + + + + + + + + + + + + + + Potential difference between the orifice and the skimmer in volts. + MS + MS:1000875 + declustering potential + + + + + Potential difference between the orifice and the skimmer in volts. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Potential difference between the sampling cone/orifice in volts. + MS + MS:1000876 + cone voltage + + + + + Potential difference between the sampling cone/orifice in volts. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Potential difference setting of the tube lens in volts. + MS + MS:1000877 + tube lens voltage + + + + + Potential difference setting of the tube lens in volts. + PSI:MS + + + + + + + + + An identifier/accession number to an external reference database. + MS + MS:1000878 + external reference identifier + + + + + An identifier/accession number to an external reference database. + PSI:MS + + + + + + + + + + + + + + + A unique identifier for a publication in the PubMed database (MIR:00000015). + MS + MS:1000879 + PubMed identifier + + + + + A unique identifier for a publication in the PubMed database (MIR:00000015). + PSI:MS + + + + + + + + + + + + + + + + + + + + + The duration of intervals between scanning, during which the instrument configuration is switched. + MS + MS:1000880 + interchannel delay + + + + + The duration of intervals between scanning, during which the instrument configuration is switched. + PSI:MS + + + + + + + + + + + + + + Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. + MS + MS:1000881 + molecular entity + + + + + Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. + https://en.wikipedia.org/wiki/Molecular_entity + + + + + + + + + A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene. + MS + MS:1000882 + protein + + + + + A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene. + PSI:MS + + + + + + + + + + + + + + + A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN). + MS + MS:1000883 + protein short name + + + + + A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN). + PSI:MS + + + + + + + + + + + + + + + An nonphysical characterstic attributed to a specific protein. + MS + MS:1000884 + protein attribute + + + + + An nonphysical characterstic attributed to a specific protein. + PSI:MS + + + + + + + + + + + + + + + + Identifier for a specific protein in a database. + MS + MS:1000885 + protein accession + + + + + Identifier for a specific protein in a database. + PSI:MS + + + + + + + + + + + + + + + A long name describing the function of the protein. + MS + MS:1000886 + protein name + + + + + A long name describing the function of the protein. + PSI:MS + + + + + + + + + + + + + + Nonphysical characteristic attributed to a peptide. + MS + MS:1000887 + peptide attribute + + + + + Nonphysical characteristic attributed to a peptide. + PSI:MS + + + + + + + + + + + + + + + Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away. + MS + MS:1000888 + stripped peptide sequence + + + + + Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away. + PSI:MS + + + + + + + + + + + + + + + Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present. + MS + MS:1000889 + Make it more general as there are actually many other ways to display a modified peptide sequence. + peptidoform sequence + + + + + Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present. + PSI:MS + + + + + + + + + A state description of how a peptide might be isotopically or isobarically labelled. + MS + MS:1000890 + peptidoform labeling state + + + + + A state description of how a peptide might be isotopically or isobarically labelled. + PSI:MS + + + + + + + + + A peptide that has been created or labelled with some heavier-than-usual isotopes. + MS + MS:1000891 + heavy labeled peptidoform + + + + + A peptide that has been created or labelled with some heavier-than-usual isotopes. + PSI:MS + + + + + + + + + A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy". + light labeled peptide + MS + MS:1000892 + unlabeled peptidoform + + + + + A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy". + PSI:MS + + + + + + + + + + + + + + + An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. + MS + MS:1000893 + peptidoform group label + + + + + An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + A time interval from the start of chromatography when an analyte exits a chromatographic column. + MS + MS:1000894 + retention time + + + + + A time interval from the start of chromatography when an analyte exits a chromatographic column. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup. + MS + MS:1000895 + local retention time + + + + + A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup. + MS + MS:1000896 + normalized retention time + + + + + A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application. + MS + MS:1000897 + predicted retention time + + + + + A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application. + PSI:MS + + + + + + + + + + + + + + Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence. + MS + MS:1000898 + standard + + + + + Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence. + PSI:MS + + + + + + + + + A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard. + MS + MS:1000899 + de facto standard + + + + + A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard. + PSI:MS + + + + + + + + + A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result. + MS + MS:1000900 + minimum information standard + + + + + A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result. + PSI:MS + + + + + + + + + A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column. + MS + MS:1000901 + retention time normalization standard + + + + + A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column. + PSI:MS + + + + + + + + + The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column. + MS + MS:1000902 + H-PINS retention time normalization standard + + + + + The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column. + DOI:10.1074/mcp.M800569-MCP200 + PMID:19411281 + + + + + + + + + + + + + + + The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion). + MS + MS:1000903 + product ion series ordinal + + + + + The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion). + PSI:PI + + + + + + + + + + + + + + + The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z. + MS + MS:1000904 + product ion m/z delta + + + + + The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z. + PSI:PI + + + + + + + + + + + + + + + The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries. + MS + MS:1000905 + percent of base peak times 100 + + + + + The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc. + MS + MS:1000906 + peak intensity rank + + + + + Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant. + MS + MS:1000907 + peak targeting suitability rank + + + + + Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant. + PSI:MS + + + + + + + + + + + + + + A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely. + reaction + MS + MS:1000908 + transition + + + + + A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely. + PSI:MS + + + + + + + + + + + + + + The strategy used to validate that a transition is effective. + MS + MS:1000909 + transition validation method + + + + + The strategy used to validate that a transition is effective. + PSI:MS + + + + + + + + + The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined. + MS + MS:1000910 + transition optimized on specified instrument + + + + + The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined. + PSI:MS + + + + + + + + + The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. + MS + MS:1000911 + transition validated with an MS/MS spectrum on specified instrument + + + + + The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. + PSI:MS + + + + + + + + + The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad). + MS + MS:1000912 + transition purported from an MS/MS spectrum on a different, specified instrument + + + + + The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad). + PSI:MS + + + + + + + + + The transition has been predicted by informatics software without any direct spectral evidence. + MS + MS:1000913 + transition predicted by informatic analysis + + + + + The transition has been predicted by informatics software without any direct spectral evidence. + PSI:MS + + + + + + + + + + A file format that has two or more columns of tabular data where each column is separated by a TAB character. + MS + MS:1000914 + tab delimited text format + + + + + A file format that has two or more columns of tabular data where each column is separated by a TAB character. + PSI:MS + + + + + + + + + + + + + + An attribute of a window in time about which a peptide might elute from the column. + MS + MS:1000915 + retention time window attribute + + + + + An attribute of a window in time about which a peptide might elute from the column. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time. + MS + MS:1000916 + retention time window lower offset + + + + + The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time. + MS + MS:1000917 + retention time window upper offset + + + + + The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time. + PSI:MS + + + + + + + + + + + + + + A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically. + MS + MS:1000918 + target list + + + + + A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically. + PSI:MS + + + + + + + + + + + + + + A priority setting specifying whether included or excluded targets have priority over the other. + MS + MS:1000919 + target inclusion exclusion priority + + + + + A priority setting specifying whether included or excluded targets have priority over the other. + PSI:MS + + + + + + + + + A priority setting specifying that included targets have priority over the excluded targets if there is a conflict. + MS + MS:1000920 + includes supersede excludes + + + + + A priority setting specifying that included targets have priority over the excluded targets if there is a conflict. + PSI:MS + + + + + + + + + A priority setting specifying that excluded targets have priority over the included targets if there is a conflict. + MS + MS:1000921 + excludes supersede includes + + + + + A priority setting specifying that excluded targets have priority over the included targets if there is a conflict. + PSI:MS + + + + + + + + + + Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington. + MS + MS:1000922 + Skyline + + + + + Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington. + https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default + + + + + + + + + Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology. + MS + MS:1000923 + TIQAM + + + + + Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology. + http://tools.proteomecenter.org/TIQAM/TIQAM.html + + + + + + + + OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. + MS:1000872 + MS + MS:1000924 + This term was made obsolete because it was redundant with an existing term (MS:1000872). + MaRiMba + true + + + + + OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology. + http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba + + + + + + + + + Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology. + MS + MS:1000925 + ATAQS + + + + + Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology. + PSI:MS + + + + + + + + + + + + + + + The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1. + MS + MS:1000926 + product interpretation rank + + + + + The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The length of time spent filling an ion trapping device. + MS + MS:1000927 + ion injection time + + + + + The length of time spent filling an ion trapping device. + PSI:MS + + + + + + + + + A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample. + MS + MS:1000928 + calibration spectrum + + + + + A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample. + PSI:MS + + + + + + + + + Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger. + MS + MS:1000929 + Shimadzu Biotech nativeID format + + + + + Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Shimadzu Biotech format. + MS + MS:1000930 + Shimadzu Biotech database entity + + + + + Shimadzu Biotech format. + PSI:MS + + + + + + + + + Applied Biosystems|MDS SCIEX QTRAP 5500. + MS + MS:1000931 + QTRAP 5500 + + + + + Applied Biosystems|MDS SCIEX QTRAP 5500. + PSI:MS + + + + + + + + + SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer. + MS + MS:1000932 + TripleTOF 5600 + + + + + SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer. + PSI:MS + + + + + + + + + + + + + + + Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation. + MS + MS:1000933 + protein modifications + + + + + Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation. + PSI:MS + + + + + + + + + + + + + + + Name of the gene from which the protein is translated. + MS + MS:1000934 + gene name + + + + + Name of the gene from which the protein is translated. + PSI:MS + + + + + + + + + The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1000935 + 6470A Triple Quadrupole LC/MS + + + + + The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1000936 + 6470B Triple Quadrupole LC/MS + + + + + The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1000937 + 6495C Triple Quadrupole LC/MS + + + + + The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + + + + + + Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra. + MS + MS:1001000 + spectrum interpretation + + + + + Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001005 + SEQUEST:CleavesAt + + + + + + + + + SEQUEST View Input Parameters. + MS + MS:1001006 + SEQUEST:ViewCV + + + + + SEQUEST View Input Parameters. + PSI:PI + + + + + + + + + + + + + + + Number of peptide results to show. + MS + MS:1001007 + SEQUEST:OutputLines + + + + + Number of peptide results to show. + PSI:MS + + + + + + + + + + + + + + + Number of full protein descriptions to show for top N peptides. + MS + MS:1001009 + SEQUEST:DescriptionLines + + + + + Number of full protein descriptions to show for top N peptides. + PSI:MS + + + + + + + + + A de novo sequencing search (without database). + MS + MS:1001010 + de novo search + + + + + A de novo sequencing search (without database). + PSI:PI + + + + + + + + + Details about the database searched. + MS + MS:1001011 + search database details + + + + + Details about the database searched. + PSI:PI + + + + + + + + + + + + + + + The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other). + MS + MS:1001012 + database source + + + + + The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other). + PSI:PI + + + + + + + + + The name of the search database (nr, SwissProt or est_human). + MS + MS:1001013 + database name + + + + + The name of the search database (nr, SwissProt or est_human). + PSI:PI + + + + + + + + + OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view. + MS + MS:1001014 + database local file path + true + + + + + OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view. + PSI:PI + + + + + + + + + + + + + + + URI, from where the search database was originally downloaded. + MS + MS:1001015 + database original uri + + + + + URI, from where the search database was originally downloaded. + PSI:PI + + + + + + + + + + + + + + + Version of the search database. In mzIdentML use the attribute instead. + MS + MS:1001016 + database version + + + + + Version of the search database. In mzIdentML use the attribute instead. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term. + MS + MS:1001017 + release date + + + + + Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term. + PSI:PI + + + + + + + + + Database containing amino acid or nucleic acid sequences. + MS + MS:1001018 + database type + + + + + Database containing amino acid or nucleic acid sequences. + PSI:PI + + + + + + + + + Was there filtering used on the database. + MS + MS:1001019 + database filtering + + + + + Was there filtering used on the database. + PSI:PI + + + + + + + + + A taxonomy filter was to the database search. + MS + MS:1001020 + DB filter taxonomy + + + + + A taxonomy filter was to the database search. + PSI:PI + + + + + + + + + Filtering applied specifically by accession number pattern. + MS + MS:1001021 + DB filter on accession numbers + + + + + Filtering applied specifically by accession number pattern. + PSI:PI + + + + + + + + + Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value. + MS + MS:1001022 + DB MW filter + + + + + Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value. + PSI:PI + + + + + + + + + Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value. + MS + MS:1001023 + DB PI filter + + + + + Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value. + PSI:PI + + + + + + + + + The translated open reading frames from a nucleotide database considered in the search (range: 1-6). + MS + MS:1001024 + translation frame + + + + + The translated open reading frames from a nucleotide database considered in the search (range: 1-6). + PSI:PI + + + + + + + + + + + + + + + The translation table used to translate the nucleotides to amino acids. + MS + MS:1001025 + translation table + + + + + The translation table used to translate the nucleotides to amino acids. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001026 + SEQUEST:NormalizeXCorrValues + + + + + + + + + Filtering applied specifically by amino acid sequence pattern. + MS + MS:1001027 + DB filter on sequence pattern + + + + + Filtering applied specifically by amino acid sequence pattern. + PSI:PI + + + + + + + + + + + + + + + String in the header of a sequence entry for that entry to be searched. + MS + MS:1001028 + SEQUEST:SequenceHeaderFilter + + + + + String in the header of a sequence entry for that entry to be searched. + PSI:MS + + + + + + + + + + + + + + + The number of sequences (proteins / nucleotides) from the database search after filtering. + MS + MS:1001029 + number of sequences searched + + + + + The number of sequences (proteins / nucleotides) from the database search after filtering. + PSI:PI + + + + + + + + + + + + + + + + Number of peptide seqs compared to each spectrum. + MS + MS:1001030 + number of peptide seqs compared to each spectrum + + + + + Number of peptide seqs compared to each spectrum. + PSI:PI + + + + + + + + + A search using a library of spectra. + MS + MS:1001031 + spectral library search + + + + + A search using a library of spectra. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001032 + SEQUEST:SequencePartialFilter + + + + + + + + + OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run. + MS + MS:1001035 + date / time search performed + true + + + + + OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run. + PSI:PI + + + + + + + + + + + + + + + The time taken to complete the search in seconds. + MS + MS:1001036 + search time taken + + + + + The time taken to complete the search in seconds. + PSI:PI + + + + + + + + + + + + + + + Flag indicating that fragment ions should be shown. + MS + MS:1001037 + SEQUEST:ShowFragmentIons + + + + + Flag indicating that fragment ions should be shown. + PSI:MS + + + + + + + + + + + + + + + Specify depth as value of the CVParam. + MS + MS:1001038 + SEQUEST:Consensus + + + + + Specify depth as value of the CVParam. + PSI:PI + + + + + + + + + Type of the source file, the mzIdentML was created from. + MS + MS:1001040 + intermediate analysis format + + + + + Type of the source file, the mzIdentML was created from. + PSI:PI + + + + + + + + + SEQUEST View / Sort Input Parameters. + MS + MS:1001041 + SEQUEST:sortCV + + + + + SEQUEST View / Sort Input Parameters. + PSI:PI + + + + + + + + + + + + + + + Specify "number of dtas shown" as value of the CVParam. + MS + MS:1001042 + SEQUEST:LimitTo + + + + + Specify "number of dtas shown" as value of the CVParam. + PSI:PI + + + + + + + + + Details of cleavage agent (enzyme). + MS + MS:1001044 + cleavage agent details + + + + + Details of cleavage agent (enzyme). + PSI:PI + + + + + + + + + The name of the cleavage agent. + MS + MS:1001045 + cleavage agent name + + + + + The name of the cleavage agent. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results by the delta of the normalized correlation score. + MS + MS:1001046 + SEQUEST:sort by dCn + + + + + Sort order of SEQUEST search results by the delta of the normalized correlation score. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M. + MS + MS:1001047 + SEQUEST:sort by dM + + + + + Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the ions. + MS + MS:1001048 + SEQUEST:sort by Ions + + + + + Sort order of SEQUEST search results given by the ions. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the mass of the protonated ion. + MS + MS:1001049 + SEQUEST:sort by MH+ + + + + + Sort order of SEQUEST search results given by the mass of the protonated ion. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the probability. + MS + MS:1001050 + SEQUEST:sort by P + + + + + Sort order of SEQUEST search results given by the probability. + PSI:PI + + + + + + + + + + + + + + OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any. + MS + MS:1001051 + multiple enzyme combination rules + true + + + + + OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the previous amino acid. + MS + MS:1001052 + SEQUEST:sort by PreviousAminoAcid + + + + + Sort order of SEQUEST search results given by the previous amino acid. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the reference. + MS + MS:1001053 + SEQUEST:sort by Ref + + + + + Sort order of SEQUEST search results given by the reference. + PSI:PI + + + + + + + + + + + + + + Modification parameters for the search engine run. + MS + MS:1001055 + modification parameters + + + + + Modification parameters for the search engine run. + PSI:PI + + + + + + + + + The specificity rules for the modifications applied by the search engine. + MS + MS:1001056 + modification specificity rule + + + + + The specificity rules for the modifications applied by the search engine. + PSI:PI + + + + + + + + + OBSOLETE: Tolerance on types. + MS + MS:1001057 + tolerance on types + true + + + + + OBSOLETE: Tolerance on types. + PSI:PI + + + + + + + + + The quality estimation was done manually. + MS + MS:1001058 + quality estimation by manual validation + + + + + The quality estimation was done manually. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide). + MS + MS:1001059 + SEQUEST:sort by RSp + + + + + Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide). + PSI:PI + + + + + + + + + Method for quality estimation (manually or with decoy database). + MS + MS:1001060 + quality estimation method details + + + + + Method for quality estimation (manually or with decoy database). + PSI:PI + + + + + + + + + OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD. + MS:1000336 + MS + MS:1001061 + neutral loss + true + + + + + OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD. + PSI:PI + + + + + + + + + Mascot MGF file format. + MS + MS:1001062 + Mascot MGF format + + + + + Mascot MGF file format. + PSI:MS + + + + + + + + + OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms. + MS:1001961 + MS + MS:1001065 + This term was made obsolete and is replaced by the term (MS:1001961). + TODOscoring model + true + + + + + OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms. + PSI:PI + + + + + + + + + The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine. + MS + MS:1001066 + ions series considered in search + + + + + The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results by the Sp score. + MS + MS:1001068 + SEQUEST:sort by Sp + + + + + Sort order of SEQUEST search results by the Sp score. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the total ion current. + MS + MS:1001069 + SEQUEST:sort by TIC + + + + + Sort order of SEQUEST search results given by the total ion current. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the scan number. + MS + MS:1001070 + SEQUEST:sort by Scan + + + + + Sort order of SEQUEST search results given by the scan number. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the sequence. + MS + MS:1001071 + SEQUEST:sort by Sequence + + + + + Sort order of SEQUEST search results given by the sequence. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the SEQUEST result 'Sf'. + MS + MS:1001072 + SEQUEST:sort by Sf + + + + + Sort order of SEQUEST search results given by the SEQUEST result 'Sf'. + PSI:PI + + + + + + + + + Database contains amino acid sequences. + MS + MS:1001073 + database type amino acid + + + + + Database contains amino acid sequences. + PSI:PI + + + + + + + + + Database contains nucleic acid sequences. + MS + MS:1001079 + database type nucleotide + + + + + Database contains nucleic acid sequences. + PSI:PI + + + + + + + + + Enumeration of type of search value (i.e. from PMF, sequence tag, MS2). + MS + MS:1001080 + search type + + + + + Enumeration of type of search value (i.e. from PMF, sequence tag, MS2). + PSI:PI + + + + + + + + + A peptide mass fingerprint search. + MS + MS:1001081 + pmf search + + + + + A peptide mass fingerprint search. + PSI:PI + + + + + + + + + A sequence tag search. + MS + MS:1001082 + tag search + + + + + A sequence tag search. + PSI:PI + + + + + + + + + An MS2 search (with fragment ions). + MS + MS:1001083 + ms-ms search + + + + + An MS2 search (with fragment ions). + PSI:PI + + + + + + + + + Non-redundant GenBank sequence database. + MS + MS:1001084 + database nr + + + + + Non-redundant GenBank sequence database. + PSI:PI + + + + + + + + + Protein level information. + MS + MS:1001085 + protein-level identification attribute + + + + + Protein level information. + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results by the correlation score. + MS + MS:1001086 + SEQUEST:sort by XCorr + + + + + Sort order of SEQUEST search results by the correlation score. + PSI:PI + + + + + + + + + SEQUEST View / Process Input Parameters. + MS + MS:1001087 + SEQUEST:ProcessCV + + + + + SEQUEST View / Process Input Parameters. + PSI:PI + + + + + + + + + + + + + + + + The protein description line from the sequence entry in the source database FASTA file. + MS + MS:1001088 + protein description + + + + + The protein description line from the sequence entry in the source database FASTA file. + PSI:PI + + + + + + + + + + + + + + + + + The taxonomy of the resultant molecule from the search. + MS + MS:1001089 + molecule taxonomy + + + + + The taxonomy of the resultant molecule from the search. + PSI:PI + + + + + + + + + OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT). + MS:1001467 + MS:1001468 + MS:1001469 + MS:1001470 + MS + MS:1001090 + taxonomy nomenclature + true + + + + + OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT). + PSI:PI + + + + + + + + + MS + MS:1001091 + This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956). + NoEnzyme + true + + + + + + + + + Identification confidence metric for a peptide. + MS + MS:1001092 + peptide sequence-level identification statistic + + + + + Identification confidence metric for a peptide. + PSI:PI + + + + + + + + + + + + + + + The percent coverage for the protein based upon the matched peptide sequences (can be calculated). + MS + MS:1001093 + sequence coverage + + + + + The percent coverage for the protein based upon the matched peptide sequences (can be calculated). + PSI:PI + + + + + + + + + + + + + + + Sort order of SEQUEST search results given by the charge. + MS + MS:1001094 + SEQUEST:sort by z + + + + + Sort order of SEQUEST search results given by the charge. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001095 + SEQUEST:ProcessAll + + + + + + + + + + + + + + + Specify "percentage" as value of the CVParam. + MS + MS:1001096 + SEQUEST:TopPercentMostIntense + + + + + Specify "percentage" as value of the CVParam. + PSI:PI + + + + + + + + + + + + + + + This counts distinct sequences hitting the protein without regard to a minimal confidence threshold. + MS + MS:1001097 + distinct peptide sequences + + + + + This counts distinct sequences hitting the protein without regard to a minimal confidence threshold. + PSI:PI + + + + + + + + + + + + + + + This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere. + MS + MS:1001098 + confident distinct peptide sequences + + + + + This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere. + PSI:PI + + + + + + + + + + + + + + + The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than. + MS + MS:1001099 + confident peptide qualification + + + + + The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than. + PSI:PI + + + + + + + + + + + + + + + This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere. + MS + MS:1001100 + confident peptide sequence number + + + + + This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere. + PSI:PI + + + + + + + + + Protein group or subset relationships. + MS + MS:1001101 + protein group or subset relationship + + + + + Protein group or subset relationships. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001102 + SEQUEST:Chromatogram + + + + + + + + + + + + + + + MS + MS:1001103 + SEQUEST:InfoAndLog + + + + + + + + + The name of the UniProtKB/Swiss-Prot knowledgebase. + MS + MS:1001104 + database UniProtKB/Swiss-Prot + + + + + The name of the UniProtKB/Swiss-Prot knowledgebase. + PSI:PI + + + + + + + + + Peptide level information. + MS + MS:1001105 + peptide sequence-level identification attribute + + + + + Peptide level information. + PSI:PI + + + + + + + + + + + + + + + Specify "number" as value of the CVParam. + MS + MS:1001106 + SEQUEST:TopNumber + + + + + Specify "number" as value of the CVParam. + PSI:PI + + + + + + + + + Source file for this mzIdentML was a data set in a database. + MS + MS:1001107 + data stored in database + + + + + Source file for this mzIdentML was a data set in a database. + PSI:PI + + + + + + + + + Parameter information, type of product: a ion with charge on the N-terminal side. + MS + MS:1001108 + param: a ion + + + + + Parameter information, type of product: a ion with charge on the N-terminal side. + PSI:PI + + + + + + + + + + + + + + + Specify cull string as value of the CVParam. + MS + MS:1001109 + SEQUEST:CullTo + + + + + Specify cull string as value of the CVParam. + PSI:PI + + + + + + + + + SEQUEST Mode Input Parameters. + MS + MS:1001110 + SEQUEST:modeCV + + + + + SEQUEST Mode Input Parameters. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001111 + SEQUEST:Full + + + + + + + + + + + + + + + + Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein. + MS + MS:1001112 + n-terminal flanking residue + + + + + Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein. + PSI:PI + + + + + + + + + + + + + + + + Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein. + MS + MS:1001113 + c-terminal flanking residue + + + + + Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + OBSOLETE Retention time of the spectrum from the source file. + MS + MS:1001114 + This term was made obsolete because scan start time (MS:1000016) should be used instead. + retention time(s) + true + + + + + OBSOLETE Retention time of the spectrum from the source file. + PSI:PI + + + + + + + + OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData. + MS + MS:1001115 + This former purgatory term was made obsolete. + scan number(s) + true + + + + + OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData. + PSI:PI + + + + + + + + + Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group). + MS + MS:1001116 + single protein identification statistic + + + + + Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group). + PSI:PI + + + + + + + + + + + + + + + + + + + + + The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier. + MS + MS:1001117 + theoretical mass + + + + + The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier. + PSI:PI + + + + + + + + + Parameter information, type of product: b ion with charge on the N-terminal side. + MS + MS:1001118 + param: b ion + + + + + Parameter information, type of product: b ion with charge on the N-terminal side. + PSI:PI + + + + + + + + + Parameter information, type of product: c ion with charge on the N-terminal side. + MS + MS:1001119 + param: c ion + + + + + Parameter information, type of product: c ion with charge on the N-terminal side. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001120 + SEQUEST:FormatAndLinks + + + + + + + + + + + + + + + The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count. + MS + MS:1001121 + number of matched peaks + + + + + The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count. + PSI:PI + + + + + + + + + The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb). + MS + MS:1001122 + ions series considered + + + + + The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb). + PSI:PI + + + + + + + + + + + + + + + The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't. + MS + MS:1001123 + number of peaks used + + + + + The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't. + PSI:PI + + + + + + + + + + + + + + + The number of peaks from the original peaks listed that were submitted to the search engine. + MS + MS:1001124 + number of peaks submitted + + + + + The number of peaks from the original peaks listed that were submitted to the search engine. + PSI:PI + + + + + + + + + + + + + + + + Result of quality estimation: decision of a manual validation. + MS + MS:1001125 + manual validation + + + + + Result of quality estimation: decision of a manual validation. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001126 + SEQUEST:Fast + + + + + + + + + Accessions Containing Sequence - Accessions for each protein containing this peptide. + MS + MS:1001127 + peptide sharing details + + + + + Accessions Containing Sequence - Accessions for each protein containing this peptide. + PSI:PI + + + + + + + + + SEQUEST Select Input Parameters. + MS + MS:1001128 + SEQUEST:selectCV + + + + + SEQUEST Select Input Parameters. + PSI:PI + + + + + + + + + + + + + + Quantification information. + MS + MS:1001129 + quantification information + + + + + Quantification information. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE Peptide raw area. + MS + MS:1001130 + This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844). + peptide raw area + true + + + + + OBSOLETE Peptide raw area. + PSI:PI + + + + + + + + + + + + + + + Error on peptide area. + MS + MS:1001131 + error on peptide area + + + + + Error on peptide area. + PSI:PI + + + + + + + + + + + + + + + Peptide ratio. + MS + MS:1001132 + peptide ratio + + + + + Peptide ratio. + PSI:PI + + + + + + + + + + + + + + + Error on peptide ratio. + MS + MS:1001133 + error on peptide ratio + + + + + Error on peptide ratio. + PSI:PI + + + + + + + + + + + + + + + Protein ratio. + MS + MS:1001134 + protein ratio + + + + + Protein ratio. + PSI:PI + + + + + + + + + + + + + + + Error on protein ratio. + MS + MS:1001135 + error on protein ratio + + + + + Error on protein ratio. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE P-value (protein diff from 1 randomly). + MS + MS:1001136 + This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855). + p-value (protein diff from 1 randomly) + true + + + + + OBSOLETE P-value (protein diff from 1 randomly). + PSI:PI + + + + + + + + + + + + + + + Absolute quantity in terms of real concentration or molecule copy number in sample. + MS + MS:1001137 + absolute quantity + + + + + Absolute quantity in terms of real concentration or molecule copy number in sample. + PSI:PI + + + + + + + + + + + + + + + Error on absolute quantity. + MS + MS:1001138 + error on absolute quantity + + + + + Error on absolute quantity. + PSI:PI + + + + + + + + + + Quantitation software name. + MS + MS:1001139 + quantitation software name + + + + + Quantitation software name. + PSI:PI + + + + + + + + + OBSOLETE Quantitation software version. + MS + MS:1001140 + This term was made obsolete because part of mzQuantML schema. + quantitation software version + true + + + + + OBSOLETE Quantitation software version. + PSI:PI + + + + + + + + + + + + + + + The intensity of the precursor ion. + MS + MS:1001141 + intensity of precursor ion + + + + + The intensity of the precursor ion. + PSI:PI + + + + + + + + + International Protein Index database for Homo sapiens sequences. + MS + MS:1001142 + database IPI_human + + + + + International Protein Index database for Homo sapiens sequences. + PSI:PI + + + + + + + + + Search engine specific peptide spectrum match scores. + MS + MS:1001143 + PSM-level search engine specific statistic + + + + + Search engine specific peptide spectrum match scores. + PSI:PI + + + + + + + + + MS + MS:1001144 + SEQUEST:SelectDefault + + + + + + + + + SEQUEST Select Advanced Input Parameters. + MS + MS:1001145 + SEQUEST:SelectAdvancedCV + + + + + SEQUEST Select Advanced Input Parameters. + PSI:PI + + + + + + + + + Ion a-NH3 parameter information, type of product: a ion with lost ammonia. + MS + MS:1001146 + param: a ion-NH3 DEPRECATED + + + + + Ion a-NH3 parameter information, type of product: a ion with lost ammonia. + PSI:PI + + + + + + + + + + MS + MS:1001147 + protein ambiguity group result details + + + + + + + + + Ion a-H2O if a significant and fragment includes STED. + MS + MS:1001148 + param: a ion-H2O DEPRECATED + + + + + Ion a-H2O if a significant and fragment includes STED. + PSI:PI + + + + + + + + + Ion b-NH3 parameter information, type of product: b ion with lost ammonia. + MS + MS:1001149 + param: b ion-NH3 DEPRECATED + + + + + Ion b-NH3 parameter information, type of product: b ion with lost ammonia. + PSI:PI + + + + + + + + + Ion b-H2O if b significant and fragment includes STED. + MS + MS:1001150 + param: b ion-H2O DEPRECATED + + + + + Ion b-H2O if b significant and fragment includes STED. + PSI:PI + + + + + + + + + Ion y-NH3 parameter information, type of product: y ion with lost ammonia. + MS + MS:1001151 + param: y ion-NH3 DEPRECATED + + + + + Ion y-NH3 parameter information, type of product: y ion with lost ammonia. + PSI:PI + + + + + + + + + MS + MS:1001152 + This term was made obsolete - use MS:1001262 and MS:1002455 instead. + param: y ion-H2O DEPRECATED + + + + + + + + + Search engine specific scores. + MS + MS:1001153 + search engine specific score + + + + + Search engine specific scores. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Probability'. + MS + MS:1001154 + SEQUEST:probability + + + + + The SEQUEST result 'Probability'. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The SEQUEST result 'XCorr'. + MS + MS:1001155 + SEQUEST:xcorr + + + + + The SEQUEST result 'XCorr'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'DeltaCn'. + MS + MS:1001156 + SEQUEST:deltacn + + + + + The SEQUEST result 'DeltaCn'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Sp' (protein). + MS + MS:1001157 + SEQUEST:sp + + + + + The SEQUEST result 'Sp' (protein). + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001158 + SEQUEST:Uniq + + + + + + + + + + + + + + + The SEQUEST result 'Expectation value'. + MS + MS:1001159 + SEQUEST:expectation value + + + + + The SEQUEST result 'Expectation value'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Sf'. + MS + MS:1001160 + SEQUEST:sf + + + + + The SEQUEST result 'Sf'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Matched Ions'. + MS + MS:1001161 + SEQUEST:matched ions + + + + + The SEQUEST result 'Matched Ions'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Total Ions'. + MS + MS:1001162 + SEQUEST:total ions + + + + + The SEQUEST result 'Total Ions'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Consensus Score'. + MS + MS:1001163 + SEQUEST:consensus score + + + + + The SEQUEST result 'Consensus Score'. + PSI:PI + + + + + + + + + + + + + + + + The Paragon result 'Unused ProtScore'. + MS + MS:1001164 + Paragon:unused protscore + + + + + The Paragon result 'Unused ProtScore'. + PSI:PI + + + + + + + + + + + + + + + + The Paragon result 'Total ProtScore'. + MS + MS:1001165 + Paragon:total protscore + + + + + The Paragon result 'Total ProtScore'. + PSI:PI + + + + + + + + + + + + + + + The Paragon result 'Score'. + MS + MS:1001166 + Paragon:score + + + + + The Paragon result 'Score'. + PSI:PI + + + + + + + + + + + + + + + The Paragon result 'Confidence'. + MS + MS:1001167 + Paragon:confidence + + + + + The Paragon result 'Confidence'. + PSI:PI + + + + + + + + + + + + + + + The Paragon result 'Expression Error Factor'. + MS + MS:1001168 + Paragon:expression error factor + + + + + The Paragon result 'Expression Error Factor'. + PSI:PI + + + + + + + + + + + + + + + The Paragon result 'Expression change P-value'. + MS + MS:1001169 + Paragon:expression change p-value + + + + + The Paragon result 'Expression change P-value'. + PSI:PI + + + + + + + + + + + + + + + The Paragon result 'Contrib'. + MS + MS:1001170 + Paragon:contrib + + + + + The Paragon result 'Contrib'. + PSI:PI + + + + + + + + + + + + + + + The Mascot result 'Score'. + MS + MS:1001171 + Mascot:score + + + + + The Mascot result 'Score'. + PSI:PI + + + + + + + + + + + + + + + The Mascot result 'expectation value'. + MS + MS:1001172 + Mascot:expectation value + + + + + The Mascot result 'expectation value'. + PSI:PI + + + + + + + + + + + + + + + The Mascot result 'Matched ions'. + MS + MS:1001173 + Mascot:matched ions + + + + + The Mascot result 'Matched ions'. + PSI:PI + + + + + + + + + + + + + + + The Mascot result 'Total ions'. + MS + MS:1001174 + Mascot:total ions + + + + + The Mascot result 'Total ions'. + PSI:PI + + + + + + + + + A peptide matching multiple proteins. + MS + MS:1001175 + peptide shared in multiple proteins + + + + + A peptide matching multiple proteins. + PSI:PI + + + + + + + + + Regular expression for Trypsin. + MS + MS:1001176 + (?<=[KR])(?!P) + + + + + Regular expression for Trypsin. + PSI:PI + + + + + + + + + + + + + + + Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search. + MS + MS:1001177 + number of molecular hypothesis considered + + + + + Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search. + PSI:PI + + + + + + + + + Expressed sequence tag nucleotide sequence database. + MS + MS:1001178 + database EST + + + + + Expressed sequence tag nucleotide sequence database. + PSI:PI + + + + + + + + + + + + + + + Regular expressions for cleavage enzymes. + MS + MS:1001180 + Cleavage agent regular expression + + + + + Regular expressions for cleavage enzymes. + PSI:PI + + + + + + + + + The details of the actual run of the search. + MS + MS:1001184 + search statistics + + + + + The details of the actual run of the search. + PSI:PI + + + + + + + + + As parameter for search engine: apply the modification only at the N-terminus of a peptide. + MS + MS:1001189 + modification specificity peptide N-term + + + + + As parameter for search engine: apply the modification only at the N-terminus of a peptide. + PSI:PI + + + + + + + + + As parameter for search engine: apply the modification only at the C-terminus of a peptide. + MS + MS:1001190 + modification specificity peptide C-term + + + + + As parameter for search engine: apply the modification only at the C-terminus of a peptide. + PSI:PI + + + + + + + + + + + + + + + + OBSOLETE Quality estimation by p-value. + MS + MS:1001191 + This term was made obsolete because now is split into peptide and protein terms. + p-value + true + + + + + OBSOLETE Quality estimation by p-value. + PSI:PI + + + + + + + + + + + + + + + + Result of quality estimation: Expect value. + MS + MS:1001192 + Expect value + + + + + Result of quality estimation: Expect value. + PSI:PI + + + + + + + + + + + + + + + + Result of quality estimation: confidence score. + MS + MS:1001193 + confidence score + + + + + Result of quality estimation: confidence score. + PSI:PI + + + + + + + + + + + + + + + Quality estimation by decoy database. + MS + MS:1001194 + quality estimation with decoy database + + + + + Quality estimation by decoy database. + PSI:PI + + + + + + + + + Decoy type: Amino acids of protein sequences are used in reverse order. + MS + MS:1001195 + decoy DB type reverse + + + + + Decoy type: Amino acids of protein sequences are used in reverse order. + PSI:PI + + + + + + + + + Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass). + MS + MS:1001196 + decoy DB type randomized + + + + + Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass). + PSI:PI + + + + + + + + + Decoy database composition: database contains original (target) and decoy entries. + MS + MS:1001197 + DB composition target+decoy + + + + + Decoy database composition: database contains original (target) and decoy entries. + PSI:PI + + + + + + + + + Identification confidence metric for a protein. + MS + MS:1001198 + protein identification confidence metric + + + + + Identification confidence metric for a protein. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in Mascot DAT file format. + MS + MS:1001199 + Mascot DAT format + + + + + Source file for this mzIdentML was in Mascot DAT file format. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in SEQUEST out file format. + MS + MS:1001200 + SEQUEST out file format + + + + + Source file for this mzIdentML was in SEQUEST out file format. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + Maximum value of molecular weight filter. + MS + MS:1001201 + DB MW filter maximum + + + + + Maximum value of molecular weight filter. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + Minimum value of molecular weight filter. + MS + MS:1001202 + DB MW filter minimum + + + + + Minimum value of molecular weight filter. + PSI:PI + + + + + + + + + + + + + + + Maximum value of isoelectric point filter. + MS + MS:1001203 + DB PI filter maximum + + + + + Maximum value of isoelectric point filter. + PSI:PI + + + + + + + + + + + + + + + Minimum value of isoelectric point filter. + MS + MS:1001204 + DB PI filter minimum + + + + + Minimum value of isoelectric point filter. + PSI:PI + + + + + + + + + The name of the Mascot search engine. + MS + MS:1001207 + Mascot + + + + + The name of the Mascot search engine. + PSI:PI + + + + + + + + + The name of the SEQUEST search engine. + MS + MS:1001208 + SEQUEST + + + + + The name of the SEQUEST search engine. + PSI:PI + + + + + + + + + The name of the Phenyx search engine. + MS + MS:1001209 + Phenyx + + + + + The name of the Phenyx search engine. + PSI:PI + + + + + + + + + The type of mass difference value to be considered by the search engine (monoisotopic or average). + MS + MS:1001210 + mass type settings + + + + + The type of mass difference value to be considered by the search engine (monoisotopic or average). + PSI:PI + + + + + + + + + Mass type setting for parent mass was monoisotopic. + MS + MS:1001211 + parent mass type mono + + + + + Mass type setting for parent mass was monoisotopic. + PSI:PI + + + + + + + + + Mass type setting for parent mass was average isotopic. + MS + MS:1001212 + parent mass type average + + + + + Mass type setting for parent mass was average isotopic. + PSI:PI + + + + + + + + OBSOLETE: Scores and global result characteristics. + MS + MS:1001213 + This former purgatory term was made obsolete. + search result details + true + + + + + OBSOLETE: Scores and global result characteristics. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the global false discovery rate of proteins. + MS + MS:1001214 + protein-level global FDR + + + + + Estimation of the global false discovery rate of proteins. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Sp' in out file (peptide). + MS + MS:1001215 + SEQUEST:PeptideSp + + + + + The SEQUEST result 'Sp' in out file (peptide). + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'. + MS + MS:1001217 + SEQUEST:PeptideRankSp + + + + + The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result '#' in out file (peptide). + MS + MS:1001218 + SEQUEST:PeptideNumber + + + + + The SEQUEST result '#' in out file (peptide). + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'Id#' in out file (peptide). + MS + MS:1001219 + SEQUEST:PeptideIdnumber + + + + + The SEQUEST result 'Id#' in out file (peptide). + PSI:PI + + + + + + + + + Fragmentation information, type of product: y ion. + MS + MS:1001220 + frag: y ion + + + + + Fragmentation information, type of product: y ion. + PSI:PI + + + + + + + + + Fragmentation information like ion types. + MS + MS:1001221 + product ion attribute + + + + + Fragmentation information like ion types. + PSI:PI + + + + + + + + + Fragmentation information, type of product: b ion without water. + MS + MS:1001222 + frag: b ion - H2O + + + + + Fragmentation information, type of product: b ion without water. + PSI:PI + + + + + + + + + Fragmentation information, type of product: y ion without water. + MS + MS:1001223 + frag: y ion - H2O + + + + + Fragmentation information, type of product: y ion without water. + PSI:PI + + + + + + + + + Fragmentation information, type of product: b ion. + MS + MS:1001224 + frag: b ion + + + + + Fragmentation information, type of product: b ion. + PSI:PI + + + + + + + + + + + + + + + The m/z of the product ion. + fragment ion m/z + MS + MS:1001225 + product ion m/z + + + + + The m/z of the product ion. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The intensity of a single product ion. + fragment ion intensity + MS + MS:1001226 + product ion intensity + + + + + The intensity of a single product ion. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + The product ion m/z error. + MS + MS:1001227 + product ion m/z error + + + + + The product ion m/z error. + PSI:PI + + + + + + + + + Fragmentation information, type of product: x ion. + MS + MS:1001228 + frag: x ion + + + + + Fragmentation information, type of product: x ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: a ion. + MS + MS:1001229 + frag: a ion + + + + + Fragmentation information, type of product: a ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: z ion. + MS + MS:1001230 + frag: z ion + + + + + Fragmentation information, type of product: z ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: c ion. + MS + MS:1001231 + frag: c ion + + + + + Fragmentation information, type of product: c ion. + PSI:PI + + + + + + + + + Ion b-NH3 fragmentation information, type of product: b ion without ammonia. + MS + MS:1001232 + frag: b ion - NH3 + + + + + Ion b-NH3 fragmentation information, type of product: b ion without ammonia. + PSI:PI + + + + + + + + + Ion y-NH3 fragmentation information, type of product: y ion without ammonia. + MS + MS:1001233 + frag: y ion - NH3 + + + + + Ion y-NH3 fragmentation information, type of product: y ion without ammonia. + PSI:PI + + + + + + + + + Fragmentation information, type of product: a ion without water. + MS + MS:1001234 + frag: a ion - H2O + + + + + Fragmentation information, type of product: a ion without water. + PSI:PI + + + + + + + + + Ion a-NH3 fragmentation information, type of product: a ion without ammonia. + MS + MS:1001235 + frag: a ion - NH3 + + + + + Ion a-NH3 fragmentation information, type of product: a ion without ammonia. + PSI:PI + + + + + + + + + Fragmentation information, type of product: d ion. + MS + MS:1001236 + frag: d ion + + + + + Fragmentation information, type of product: d ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: v ion. + MS + MS:1001237 + frag: v ion + + + + + Fragmentation information, type of product: v ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: w ion. + MS + MS:1001238 + frag: w ion + + + + + Fragmentation information, type of product: w ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: immonium ion. + MS + MS:1001239 + frag: immonium ion + + + + + Fragmentation information, type of product: immonium ion. + PSI:PI + + + + + + + + + Non-identified ion. + MS + MS:1001240 + non-identified ion + + + + + Non-identified ion. + PSI:PI + + + + + + + + + Co-eluting ion. + MS + MS:1001241 + co-eluting ion + + + + + Co-eluting ion. + PSI:PI + + + + + + + + + Source file for this mzIdentML was a SEQUEST folder with its out files. + MS + MS:1001242 + SEQUEST out folder + + + + + Source file for this mzIdentML was a SEQUEST folder with its out files. + PSI:PI + + + + + + + + + Source file for this mzIdentML was a SEQUEST summary page (proteins). + MS + MS:1001243 + SEQUEST summary + + + + + Source file for this mzIdentML was a SEQUEST summary page (proteins). + PSI:PI + + + + + + + + + PerSeptive peak list file format. + MS + MS:1001245 + PerSeptive PKS format + + + + + PerSeptive peak list file format. + http://www.matrixscience.com/help/data_file_help.html#PKS + + + + + + + + + PE SCIEX peak list file format. + MS + MS:1001246 + SCIEX API III format + + + + + PE SCIEX peak list file format. + http://www.matrixscience.com/help/data_file_help.html#API + + + + + + + + + Bruker data exchange XML format. + MS + MS:1001247 + Bruker XML format + + + + + Bruker data exchange XML format. + PSI:PI + + + + + + + + + + + + + + Details describing the search input. + MS + MS:1001249 + search input details + + + + + Details describing the search input. + PSI:PI + + + + + + + + + + + + + + + + Result of quality estimation: the local FDR at the current position of a sorted list. + MS + MS:1001250 + local FDR + + + + + Result of quality estimation: the local FDR at the current position of a sorted list. + PSI:PI + + + + + + + + + + + + + + + Enzyme trypsin. + MS + MS:1001251 + Trypsin + + + + + Enzyme trypsin. + PSI:PI + + + + + + + + + Database source EBI. + MS + MS:1001252 + DB source EBI + + + + + Database source EBI. + PSI:PI + + + + + + + + + Database source NCBI. + MS + MS:1001253 + DB source NCBI + + + + + Database source NCBI. + PSI:PI + + + + + + + + + Database source UniProt. + MS + MS:1001254 + DB source UniProt + + + + + Database source UniProt. + PSI:PI + + + + + + + + + Mass type setting for fragment mass was average isotopic. + MS + MS:1001255 + fragment mass type average + + + + + Mass type setting for fragment mass was average isotopic. + PSI:PI + + + + + + + + + Mass type setting for fragment mass was monoisotopic. + MS + MS:1001256 + fragment mass type mono + + + + + Mass type setting for fragment mass was monoisotopic. + PSI:PI + + + + + + + + + Parameter information, type of product: side chain loss v ion. + MS + MS:1001257 + param: v ion + + + + + Parameter information, type of product: side chain loss v ion. + PSI:PI + + + + + + + + + Parameter information, type of product: side chain loss d ion. + MS + MS:1001258 + param: d ion + + + + + Parameter information, type of product: side chain loss d ion. + PSI:PI + + + + + + + + + Parameter information, type of product: immonium ion. + MS + MS:1001259 + param: immonium ion + + + + + Parameter information, type of product: immonium ion. + PSI:PI + + + + + + + + + Parameter information, type of product: side chain loss w ion. + MS + MS:1001260 + param: w ion + + + + + Parameter information, type of product: side chain loss w ion. + PSI:PI + + + + + + + + + Parameter information, type of product: x ion with charge on the C-terminal side. + MS + MS:1001261 + param: x ion + + + + + Parameter information, type of product: x ion with charge on the C-terminal side. + PSI:PI + + + + + + + + + Parameter information, type of product: y ion with charge on the C-terminal side. + MS + MS:1001262 + param: y ion + + + + + Parameter information, type of product: y ion with charge on the C-terminal side. + PSI:PI + + + + + + + + + Parameter information, type of product: z ion with charge on the C-terminal side. + MS + MS:1001263 + param: z ion + + + + + Parameter information, type of product: z ion with charge on the C-terminal side. + PSI:PI + + + + + + + + + Role of a Person or Organization. + MS + MS:1001266 + role type + + + + + Role of a Person or Organization. + PSI:PI + + + + + + + + + Software vendor role. + MS + MS:1001267 + software vendor + + + + + Software vendor role. + PSI:PI + + + + + + + + + + + + + + + Programmer role. + MS + MS:1001268 + programmer + + + + + Programmer role. + PSI:PI + + + + + + + + + + + + + + + Instrument vendor role. + MS + MS:1001269 + instrument vendor + + + + + Instrument vendor role. + PSI:PI + + + + + + + + + + + + + + + Lab personnel role. + MS + MS:1001270 + lab personnel + + + + + Lab personnel role. + PSI:PI + + + + + + + + + Researcher role. + MS + MS:1001271 + researcher + + + + + Researcher role. + PSI:PI + + + + + + + + + Regular expression for Arg-C. + MS + MS:1001272 + (?<=R)(?!P) + + + + + Regular expression for Arg-C. + PSI:PI + + + + + + + + + Regular expression for Asp-N. + MS + MS:1001273 + (?=[BD]) + + + + + Regular expression for Asp-N. + PSI:PI + + + + + + + + + Regular expression for Asp-N-ambic. + MS + MS:1001274 + (?=[DE]) + + + + + Regular expression for Asp-N-ambic. + PSI:PI + + + + + + + + + Source data for this mzIdentML was a ProteinScape SearchEvent. + MS + MS:1001275 + ProteinScape SearchEvent + + + + + Source data for this mzIdentML was a ProteinScape SearchEvent. + PSI:PI + + + + + + + + + Source data for this mzIdentML was a ProteinScape Gel. + MS + MS:1001276 + ProteinScape Gel + + + + + Source data for this mzIdentML was a ProteinScape Gel. + PSI:PI + + + + + + + + + + + + + + + Specify the regular expression for decoy accession numbers. + MS + MS:1001283 + decoy DB accession regexp + + + + + Specify the regular expression for decoy accession numbers. + PSI:PI + + + + + + + + + OBSOLETE The name of the database, the search database was derived from. + MS + MS:1001284 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB derived from + true + + + + + OBSOLETE The name of the database, the search database was derived from. + PSI:PI + + + + + + + + + International Protein Index database for Mus musculus sequences. + MS + MS:1001285 + database IPI_mouse + + + + + International Protein Index database for Mus musculus sequences. + PSI:PI + + + + + + + + + International Protein Index database for Rattus norvegicus sequences. + MS + MS:1001286 + database IPI_rat + + + + + International Protein Index database for Rattus norvegicus sequences. + PSI:PI + + + + + + + + + International Protein Index database for Danio rerio sequences. + MS + MS:1001287 + database IPI_zebrafish + + + + + International Protein Index database for Danio rerio sequences. + PSI:PI + + + + + + + + + International Protein Index database for Gallus gallus sequences. + MS + MS:1001288 + database IPI_chicken + + + + + International Protein Index database for Gallus gallus sequences. + PSI:PI + + + + + + + + + International Protein Index database for Bos taurus sequences. + MS + MS:1001289 + database IPI_cow + + + + + International Protein Index database for Bos taurus sequences. + PSI:PI + + + + + + + + + International Protein Index database for Arabidopsis thaliana sequences. + MS + MS:1001290 + database IPI_arabidopsis + + + + + International Protein Index database for Arabidopsis thaliana sequences. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a non-redundant GenBank sequence database. + MS + MS:1001291 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from nr + true + + + + + OBSOLETE Decoy database from a non-redundant GenBank sequence database. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus. + MS + MS:1001292 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from IPI_rat + true + + + + + OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a International Protein Index database for Mus musculus. + MS + MS:1001293 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from IPI_mouse + true + + + + + OBSOLETE Decoy database from a International Protein Index database for Mus musculus. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana. + MS + MS:1001294 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from IPI_arabidopsis + true + + + + + OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana. + PSI:PI + + + + + + + + OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database. + MS + MS:1001295 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from EST + true + + + + + OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a International Protein Index database for Danio rerio. + MS + MS:1001296 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from IPI_zebrafish + true + + + + + OBSOLETE Decoy database from a International Protein Index database for Danio rerio. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a Swiss-Prot protein sequence database. + MS + MS:1001297 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from UniProtKB/Swiss-Prot + true + + + + + OBSOLETE Decoy database from a Swiss-Prot protein sequence database. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a International Protein Index database for Gallus gallus. + MS + MS:1001298 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from IPI_chicken + true + + + + + OBSOLETE Decoy database from a International Protein Index database for Gallus gallus. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a International Protein Index database for Bos taurus. + MS + MS:1001299 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from IPI_cow + true + + + + + OBSOLETE Decoy database from a International Protein Index database for Bos taurus. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a International Protein Index database for Homo sapiens. + MS + MS:1001300 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from IPI_human + true + + + + + OBSOLETE Decoy database from a International Protein Index database for Homo sapiens. + PSI:PI + + + + + + + + + + + + + + + The rank of the protein in a list sorted by the search engine. + MS + MS:1001301 + protein rank + + + + + The rank of the protein in a list sorted by the search engine. + PSI:PI + + + + + + + + + Search engine specific input parameters. + MS + MS:1001302 + search engine specific input parameter + + + + + Search engine specific input parameters. + PSI:PI + + + + + + + + + + + + + + + Endoproteinase Arg-C. + Clostripain + Trypsin/R + MS + MS:1001303 + Arg-C + + + + + Endoproteinase Arg-C. + PSI:PI + + + + + + + + + + + + + + + Endoproteinase Asp-N. + MS + MS:1001304 + Asp-N + + + + + Endoproteinase Asp-N. + PSI:PI + + + + + + + + + + + + + + + Enzyme Asp-N, Ammonium Bicarbonate (AmBic). + MS + MS:1001305 + Asp-N_ambic + + + + + Enzyme Asp-N, Ammonium Bicarbonate (AmBic). + PSI:PI + + + + + + + + + + + + + + + Enzyme chymotrypsin. + MS + MS:1001306 + Chymotrypsin + + + + + Enzyme chymotrypsin. + PSI:PI + + + + + + + + + + + + + + + Cyanogen bromide. + MS + MS:1001307 + CNBr + + + + + Cyanogen bromide. + PSI:PI + + + + + + + + + + + + + + + Formic acid. + MS + MS:1001308 + Formic_acid + + + + + Formic acid. + PubChem_Compound:284 + + + + + + + + + + + + + + + Endoproteinase Lys-C. + Trypsin/K + MS + MS:1001309 + Lys-C + + + + + Endoproteinase Lys-C. + PSI:PI + + + + + + + + + + + + + + + Proteinase Lys-C/P. + MS + MS:1001310 + Lys-C/P + + + + + Proteinase Lys-C/P. + PSI:PI + + + + + + + + + + + + + + + PepsinA proteinase. + MS + MS:1001311 + PepsinA + + + + + PepsinA proteinase. + PSI:PI + + + + + + + + + + + + + + + Cleavage agent TrypChymo. + MS + MS:1001312 + TrypChymo + + + + + Cleavage agent TrypChymo. + PSI:PI + + + + + + + + + + + + + + + Cleavage agent Trypsin/P. + MS + MS:1001313 + Trypsin/P + + + + + Cleavage agent Trypsin/P. + PSI:PI + + + + + + + + + + + + + + + Cleavage agent V8-DE. + MS + MS:1001314 + V8-DE + + + + + Cleavage agent V8-DE. + PSI:PI + + + + + + + + + + + + + + + Cleavage agent V8-E. + MS + MS:1001315 + V8-E + + + + + Cleavage agent V8-E. + PSI:PI + + + + + + + + + + + + + + + Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05). + MS + MS:1001316 + Mascot:SigThreshold + + + + + Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05). + PSI:PI + + + + + + + + + + + + + + + The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1. + MS + MS:1001317 + Mascot:MaxProteinHits + + + + + The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1. + PSI:PI + + + + + + + + + + + + + + + Mascot protein scoring method; either 'Standard' or 'MudPIT'. + MS + MS:1001318 + Mascot:ProteinScoringMethod + + + + + Mascot protein scoring method; either 'Standard' or 'MudPIT'. + PSI:PI + + + + + + + + + + + + + + + Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed. + MS + MS:1001319 + Mascot:MinMSMSThreshold + + + + + Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed. + PSI:PI + + + + + + + + + + + + + + + If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed. + MS + MS:1001320 + Mascot:ShowHomologousProteinsWithSamePeptides + + + + + If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed. + PSI:PI + + + + + + + + + + + + + + + If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed. + MS + MS:1001321 + Mascot:ShowHomologousProteinsWithSubsetOfPeptides + + + + + If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed. + PSI:PI + + + + + + + + + + + + + + + Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits. + MS + MS:1001322 + Mascot:RequireBoldRed + + + + + Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits. + PSI:PI + + + + + + + + + + + + + + + If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use. + MS + MS:1001323 + Mascot:UseUnigeneClustering + + + + + If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use. + PSI:PI + + + + + + + + + + + + + + + If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included. + MS + MS:1001324 + Mascot:IncludeErrorTolerantMatches + + + + + If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included. + http://www.matrixscience.com/help/error_tolerant_help.html + + + + + + + + + + + + + + + If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database. + MS + MS:1001325 + Mascot:ShowDecoyMatches + + + + + If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database. + PSI:PI + + + + + + + + OBSOLETE. + MS + MS:1001326 + This former purgatory term was made obsolete. + add_others + true + + + + + OBSOLETE. + PSI:PI + + + + + + + + + + + + + + + OMSSA E-value. + MS + MS:1001328 + OMSSA:evalue + + + + + OMSSA E-value. + PSI:PI + + + + + + + + + + + + + + + OMSSA p-value. + MS + MS:1001329 + OMSSA:pvalue + + + + + OMSSA p-value. + PSI:PI + + + + + + + + + + + + + + + The X!Tandem expectation value. + MS + MS:1001330 + X!Tandem:expect + + + + + The X!Tandem expectation value. + PSI:PI + + + + + + + + + + + + + + + The X!Tandem hyperscore. + MS + MS:1001331 + X!Tandem:hyperscore + + + + + The X!Tandem hyperscore. + PSI:PI + + + + + + + + + Regular expression for Chymotrypsin. + MS + MS:1001332 + (?<=[FYWL])(?!P) + + + + + Regular expression for Chymotrypsin. + PSI:PI + + + + + + + + + Regular expression for CNBr. + MS + MS:1001333 + (?<=M) + + + + + Regular expression for CNBr. + PSI:PI + + + + + + + + + Regular expression for formic acid. + MS + MS:1001334 + ((?<=D))|((?=D)) + + + + + Regular expression for formic acid. + PSI:PI + + + + + + + + + Regular expression for Lys-C. + MS + MS:1001335 + (?<=K)(?!P) + + + + + Regular expression for Lys-C. + PSI:PI + + + + + + + + + Regular expression for Lys-C/P. + MS + MS:1001336 + (?<=K) + + + + + Regular expression for Lys-C/P. + PSI:PI + + + + + + + + + Regular expression for PepsinA. + MS + MS:1001337 + (?<=[FL]) + + + + + Regular expression for PepsinA. + PSI:PI + + + + + + + + + Regular expression for TrypChymo. + MS + MS:1001338 + (?<=[FYWLKR])(?!P) + + + + + Regular expression for TrypChymo. + PSI:PI + + + + + + + + + Regular expression for Trypsin/P. + MS + MS:1001339 + (?<=[KR]) + + + + + Regular expression for Trypsin/P. + PSI:PI + + + + + + + + + Regular expression for V8-DE. + MS + MS:1001340 + (?<=[BDEZ])(?!P) + + + + + Regular expression for V8-DE. + PSI:PI + + + + + + + + + Regular expression for V8-E. + MS + MS:1001341 + (?<=[EZ])(?!P) + + + + + Regular expression for V8-E. + PSI:PI + + + + + + + + + Details about a single database sequence. + MS + MS:1001342 + database sequence details + + + + + Details about a single database sequence. + PSI:PI + + + + + + + + + The sequence is a nucleic acid sequence. + MS + MS:1001343 + NA sequence + + + + + The sequence is a nucleic acid sequence. + PSI:PI + + + + + + + + + The sequence is a amino acid sequence. + MS + MS:1001344 + AA sequence + + + + + The sequence is a amino acid sequence. + PSI:PI + + + + + + + + + Children of this term specify the source of the mass table used. + MS + MS:1001345 + mass table source + + + + + Children of this term specify the source of the mass table used. + PSI:PI + + + + + + + + + The masses used in the mass table are taken from AAIndex. + MS + MS:1001346 + AAIndex mass table + + + + + The masses used in the mass table are taken from AAIndex. + PSI:PI + + + + + + + + + The children of this term define file formats of the sequence database used. + MS + MS:1001347 + database file formats + + + + + The children of this term define file formats of the sequence database used. + PSI:PI + + + + + + + + + The sequence database was stored in the FASTA format. + MS + MS:1001348 + FASTA format + + + + + The sequence database was stored in the FASTA format. + PSI:PI + + + + + + + + + The sequence database was stored in the Abstract Syntax Notation 1 format. + MS + MS:1001349 + ASN.1 + + + + + The sequence database was stored in the Abstract Syntax Notation 1 format. + PSI:PI + + + + + + + + + The sequence database was stored in the NCBI formatdb (*.p*) format. + MS + MS:1001350 + NCBI *.p* + + + + + The sequence database was stored in the NCBI formatdb (*.p*) format. + PSI:PI + + + + + + + + + ClustalW ALN (multiple alignment) format. + MS + MS:1001351 + clustal aln + + + + + ClustalW ALN (multiple alignment) format. + PSI:PI + + + + + + + + + EMBL entry format. + MS + MS:1001352 + embl em + + + + + EMBL entry format. + PSI:PI + + + + + + + + + The NBRF PIR was used as format. + MS + MS:1001353 + NBRF PIR + + + + + The NBRF PIR was used as format. + PSI:PI + + + + + + + + + + + + + + Root node for options for the mass table used. + MS + MS:1001354 + mass table options + + + + + Root node for options for the mass table used. + PSI:PI + + + + + + + + + Descriptions of peptides. + MS + MS:1001355 + peptide descriptions + + + + + Descriptions of peptides. + PSI:PI + + + + + + + + + Descriptions of the input spectra. + MS + MS:1001356 + spectrum descriptions + + + + + Descriptions of the input spectra. + PSI:PI + + + + + + + + + Description of the quality of the input spectrum. + MS + MS:1001357 + spectrum quality descriptions + + + + + Description of the quality of the input spectrum. + PSI:PI + + + + + + + + + + + + + + + This term reports the quality of the spectrum assigned by msmsEval. + MS + MS:1001358 + msmsEval quality + + + + + This term reports the quality of the spectrum assigned by msmsEval. + PSI:PI + + + + + + + + + + + + + + Children of this term describe ambiguous residues. + MS + MS:1001359 + ambiguous residues + + + + + Children of this term describe ambiguous residues. + PSI:PI + + + + + + + + + + + + + + + List of standard residue one letter codes which are used to replace a non-standard. + MS + MS:1001360 + alternate single letter codes + + + + + List of standard residue one letter codes which are used to replace a non-standard. + PSI:PI + + + + + + + + + + + + + + + + + + + + + List of masses a non-standard letter code is replaced with. + MS + MS:1001361 + alternate mass + + + + + List of masses a non-standard letter code is replaced with. + PSI:PI + + + + + + + + + + + + + + + The number of unmatched peaks. + MS + MS:1001362 + number of unmatched peaks + + + + + The number of unmatched peaks. + PSI:PI + + + + + + + + + A peptide matching only one. + MS + MS:1001363 + peptide unique to one protein + + + + + A peptide matching only one. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + MS + MS:1001364 + peptide sequence-level global FDR + + + + + Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + PSI:PI + + + + + + + + + Fragmentation information, type of product: internal yb ion. + MS + MS:1001365 + frag: internal yb ion + + + + + Fragmentation information, type of product: internal yb ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: internal ya ion. + MS + MS:1001366 + frag: internal ya ion + + + + + Fragmentation information, type of product: internal ya ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: z+1 ion. + MS + MS:1001367 + frag: z+1 ion + + + + + Fragmentation information, type of product: z+1 ion. + PSI:PI + + + + + + + + + Fragmentation information, type of product: z+2 ion. + MS + MS:1001368 + frag: z+2 ion + + + + + Fragmentation information, type of product: z+2 ion. + PSI:PI + + + + + + + + + Simple text file format of "m/z [intensity]" values for a PMF (or single MS2) search. + MS + MS:1001369 + text format + + + + + Simple text file format of "m/z [intensity]" values for a PMF (or single MS2) search. + PSI:PI + + + + + + + + + + + + + + + The Mascot result 'homology threshold'. + MS + MS:1001370 + Mascot:homology threshold + + + + + The Mascot result 'homology threshold'. + PSI:PI + + + + + + + + + + + + + + + The Mascot result 'identity threshold'. + MS + MS:1001371 + Mascot:identity threshold + + + + + The Mascot result 'identity threshold'. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001372 + SEQUEST:Sequences + + + + + + + + + + + + + + + SEQUEST total ion current. + MS + MS:1001373 + SEQUEST:TIC + + + + + SEQUEST total ion current. + PSI:PI + + + + + + + + + + + + + + + MS + MS:1001374 + SEQUEST:Sum + + + + + + + + + + + + + + + The instrument type parameter value in Phenyx. + MS + MS:1001375 + Phenyx:Instrument Type + + + + + The instrument type parameter value in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The selected scoring model in Phenyx. + MS + MS:1001376 + Phenyx:Scoring Model + + + + + The selected scoring model in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The default parent charge value in Phenyx. + MS + MS:1001377 + Phenyx:Default Parent Charge + + + + + The default parent charge value in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct. + MS + MS:1001378 + Phenyx:Trust Parent Charge + + + + + The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct. + PSI:PI + + + + + + + + + + + + + + + The turbo mode parameter in Phenyx. + MS + MS:1001379 + Phenyx:Turbo + + + + + The turbo mode parameter in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx. + MS + MS:1001380 + Phenyx:Turbo:ErrorTol + + + + + The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx. + PSI:PI + + + + + + + + + + + + + + + The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx. + MS + MS:1001381 + Phenyx:Turbo:Coverage + + + + + The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx. + PSI:PI + + + + + + + + + + + + + + + The list of ion series considered in the turbo mode of Phenyx. + MS + MS:1001382 + Phenyx:Turbo:Series + + + + + The list of ion series considered in the turbo mode of Phenyx. + PSI:PI + + + + + + + + + + + + + + + The minimal number of residues for a peptide to be considered for a valid identification in Phenyx. + MS + MS:1001383 + Phenyx:MinPepLength + + + + + The minimal number of residues for a peptide to be considered for a valid identification in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx. + MS + MS:1001384 + Phenyx:MinPepzscore + + + + + The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx. + MS + MS:1001385 + Phenyx:MaxPepPvalue + + + + + The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx. + MS + MS:1001386 + Phenyx:AC Score + + + + + The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used. + MS + MS:1001387 + Phenyx:Conflict Resolution + + + + + The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used. + PSI:PI + + + + + + + + + + + + + + + The primary sequence database identifier of a protein in Phenyx. + MS + MS:1001388 + Phenyx:AC + + + + + The primary sequence database identifier of a protein in Phenyx. + PSI:PI + + + + + + + + + + + + + + + A secondary sequence database identifier of a protein in Phenyx. + MS + MS:1001389 + Phenyx:ID + + + + + A secondary sequence database identifier of a protein in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The protein score of a protein match in Phenyx. + MS + MS:1001390 + Phenyx:Score + + + + + The protein score of a protein match in Phenyx. + PSI:PI + + + + + + + + + + + + + + + First number of phenyx result "#Peptides". + MS + MS:1001391 + Phenyx:Peptides1 + + + + + First number of phenyx result "#Peptides". + PSI:PI + + + + + + + + + + + + + + + Second number of phenyx result "#Peptides". + MS + MS:1001392 + Phenyx:Peptides2 + + + + + Second number of phenyx result "#Peptides". + PSI:PI + + + + + + + + + + + + + + + The value of the automatic peptide acceptance filter in Phenyx. + MS + MS:1001393 + Phenyx:Auto + + + + + The value of the automatic peptide acceptance filter in Phenyx. + PSI:PI + + + + + + + + + + + + + + + + The value of the user-defined peptide acceptance filter in Phenyx. + MS + MS:1001394 + Phenyx:User + + + + + The value of the user-defined peptide acceptance filter in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The z-score value of a peptide sequence match in Phenyx. + MS + MS:1001395 + Phenyx:Pepzscore + + + + + The z-score value of a peptide sequence match in Phenyx. + PSI:PI + + + + + + + + + + + + + + + + The p-value of a peptide sequence match in Phenyx. + MS + MS:1001396 + Phenyx:PepPvalue + + + + + The p-value of a peptide sequence match in Phenyx. + PSI:PI + + + + + + + + + + + + + + + The number of missed cleavages of a peptide sequence in Phenyx. + MS + MS:1001397 + Phenyx:NumberOfMC + + + + + The number of missed cleavages of a peptide sequence in Phenyx. + PSI:PI + + + + + + + + + + + + + + + + The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx. + MS + MS:1001398 + Phenyx:Modif + + + + + The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in OMSSA csv file format. + MS + MS:1001399 + OMSSA csv format + + + + + Source file for this mzIdentML was in OMSSA csv file format. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in OMSSA xml file format. + MS + MS:1001400 + OMSSA xml format + + + + + Source file for this mzIdentML was in OMSSA xml file format. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in X!Tandem xml file format. + MS + MS:1001401 + X!Tandem xml format + + + + + Source file for this mzIdentML was in X!Tandem xml file format. + PSI:PI + + + + + + + + + + + + + + This subsection describes terms which can describe details of spectrum identification results. + MS + MS:1001405 + spectrum identification result details + + + + + This subsection describes terms which can describe details of spectrum identification results. + PSI:PI + + + + + + + + + Parameter information, type of product: internal yb ion. + MS + MS:1001406 + param: internal yb ion + + + + + Parameter information, type of product: internal yb ion. + PSI:PI + + + + + + + + + Parameter information, type of product: internal ya ion. + MS + MS:1001407 + param: internal ya ion + + + + + Parameter information, type of product: internal ya ion. + PSI:PI + + + + + + + + + Parameter information, type of product: z+1 ion. + MS + MS:1001408 + param: z+1 ion + + + + + Parameter information, type of product: z+1 ion. + PSI:PI + + + + + + + + + Parameter information, type of product: z+2 ion. + MS + MS:1001409 + param: z+2 ion + + + + + Parameter information, type of product: z+2 ion. + PSI:PI + + + + + + + + + + + + + + + The translation start codons used to translate the nucleotides to amino acids. + MS + MS:1001410 + translation start codons + + + + + The translation start codons used to translate the nucleotides to amino acids. + PSI:PI + + + + + + + + + Specification of the search tolerance. + MS + MS:1001411 + search tolerance specification + + + + + Specification of the search tolerance. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MS + MS:1001412 + search tolerance plus value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MS + MS:1001413 + search tolerance minus value + + + + + + + + + + + + + + + OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file. + MS:1000797 + MS + MS:1001414 + MGF scans + true + + + + + OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file. + MS:1000798 + MS + MS:1001415 + MGF raw scans + true + + + + + OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE. + MS:1000796 + MS + MS:1001416 + spectrum title + true + + + + + OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE. + PSI:PI + + + + + + + + + + + + + + + SpectraST dot product of two spectra, measuring spectral similarity. + MS + MS:1001417 + SpectraST:dot + + + + + SpectraST dot product of two spectra, measuring spectral similarity. + PSI:PI + + + + + + + + + + + + + + + SpectraST measure of how much of the dot product is dominated by a few peaks. + MS + MS:1001418 + SpectraST:dot_bias + + + + + SpectraST measure of how much of the dot product is dominated by a few peaks. + PSI:PI + + + + + + + + + + + + + + + SpectraST spectrum score. + MS + MS:1001419 + SpectraST:discriminant score F + + + + + SpectraST spectrum score. + PSI:PI + + + + + + + + + + + + + + + SpectraST normalised difference between dot product of top hit and runner-up. + MS + MS:1001420 + SpectraST:delta + + + + + SpectraST normalised difference between dot product of top hit and runner-up. + PSI:PI + + + + + + + + + The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers. + MS + MS:1001421 + pepXML format + + + + + The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers. + PSI:PI + + + + + + + + + The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers. + MS + MS:1001422 + protXML format + + + + + The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers. + PSI:PI + + + + + + + + + + + + + + + A URL that describes the translation table used to translate the nucleotides to amino acids. + MS + MS:1001423 + translation table description + + + + + A URL that describes the translation table used to translate the nucleotides to amino acids. + PSI:PI + + + + + + + + + + + + + + + Name of the used method in the ProteinExtractor algorithm. + MS + MS:1001424 + ProteinExtractor:Methodname + + + + + Name of the used method in the ProteinExtractor algorithm. + PSI:PI + + + + + + + + + + + + + + + Flag indicating if a non redundant scoring should be generated. + MS + MS:1001425 + ProteinExtractor:GenerateNonRedundant + + + + + Flag indicating if a non redundant scoring should be generated. + PSI:PI + + + + + + + + + + + + + + + Flag indicating if identified proteins should be included. + MS + MS:1001426 + ProteinExtractor:IncludeIdentified + + + + + Flag indicating if identified proteins should be included. + PSI:PI + + + + + + + + + + + + + + + The maximum number of proteins to consider. + MS + MS:1001427 + ProteinExtractor:MaxNumberOfProteins + + + + + The maximum number of proteins to consider. + PSI:PI + + + + + + + + + + + + + + + The maximum considered mass for a protein. + MS + MS:1001428 + ProteinExtractor:MaxProteinMass + + + + + The maximum considered mass for a protein. + PSI:PI + + + + + + + + + + + + + + + The minimum number of proteins to consider. + MS + MS:1001429 + ProteinExtractor:MinNumberOfPeptides + + + + + The minimum number of proteins to consider. + PSI:PI + + + + + + + + + + + + + + + Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score. + MS + MS:1001430 + ProteinExtractor:UseMascot + + + + + Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score. + PSI:PI + + + + + + + + + + + + + + + Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score. + MS + MS:1001431 + ProteinExtractor:MascotPeptideScoreThreshold + + + + + Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation. + MS + MS:1001432 + ProteinExtractor:MascotUniqueScore + + + + + In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + MS + MS:1001433 + ProteinExtractor:MascotUseIdentityScore + + + + + + + + + + + + + + + Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. + MS + MS:1001434 + ProteinExtractor:MascotWeighting + + + + + Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score. + MS + MS:1001435 + ProteinExtractor:UseSequest + + + + + Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score. + PSI:PI + + + + + + + + + + + + + + + Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score. + MS + MS:1001436 + ProteinExtractor:SequestPeptideScoreThreshold + + + + + Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation. + MS + MS:1001437 + ProteinExtractor:SequestUniqueScore + + + + + In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. + MS + MS:1001438 + ProteinExtractor:SequestWeighting + + + + + Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score. + MS + MS:1001439 + ProteinExtractor:UseProteinSolver + + + + + Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score. + PSI:PI + + + + + + + + + + + + + + + Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score. + MS + MS:1001440 + ProteinExtractor:ProteinSolverPeptideScoreThreshold + + + + + Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation. + MS + MS:1001441 + ProteinExtractor:ProteinSolverUniqueScore + + + + + In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. + MS + MS:1001442 + ProteinExtractor:ProteinSolverWeighting + + + + + Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score. + MS + MS:1001443 + ProteinExtractor:UsePhenyx + + + + + Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score. + PSI:PI + + + + + + + + + + + + + + + Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score. + MS + MS:1001444 + ProteinExtractor:PhenyxPeptideScoreThreshold + + + + + Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation. + MS + MS:1001445 + ProteinExtractor:PhenyxUniqueScore + + + + + In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. + MS + MS:1001446 + ProteinExtractor:PhenyxWeighting + + + + + Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor. + DOI:10.4172/jpb.1000056 + + + + + + + + + + + + + + + False-discovery rate threshold for proteins. + MS + MS:1001447 + prot:FDR threshold + + + + + False-discovery rate threshold for proteins. + PSI:PI + + + + + + + + + + + + + + + False-discovery rate threshold for peptides. + MS + MS:1001448 + pep:FDR threshold + + + + + False-discovery rate threshold for peptides. + PSI:PI + + + + + + + + + + + + + + + Threshold for OMSSA e-value for quality estimation. + MS + MS:1001449 + OMSSA e-value threshold + + + + + Threshold for OMSSA e-value for quality estimation. + PSI:PI + + + + + + + + + Details of decoy generation and database structure. + MS + MS:1001450 + decoy DB details + + + + + Details of decoy generation and database structure. + PSI:PI + + + + + + + + + + + + + + + Name of algorithm used for decoy generation. + MS + MS:1001451 + decoy DB generation algorithm + + + + + Name of algorithm used for decoy generation. + PSI:PI + + + + + + + + + Decoy type: Amino acids of protein sequences are used in a random order. + MS + MS:1001452 + decoy DB type shuffle + + + + + Decoy type: Amino acids of protein sequences are used in a random order. + PSI:PI + + + + + + + + + Decoy database composition: database contains only decoy entries. + MS + MS:1001453 + DB composition only decoy + + + + + Decoy database composition: database contains only decoy entries. + PSI:PI + + + + + + + + + Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy). + MS + MS:1001454 + quality estimation with implicite decoy sequences + + + + + Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy). + PSI:PI + + + + + + + + + Acquisition software. + MS + MS:1001455 + acquisition software + + + + + Acquisition software. + PSI:MS + + + + + + + + + Analysis software. + MS + MS:1001456 + analysis software + + + + + Analysis software. + PSI:MS + + + + + + + + + Data processing software. + MS + MS:1001457 + data processing software + + + + + Data processing software. + PSI:MS + + + + + + + + + + + + + + Vocabularies describing the spectrum generation information. + MS + MS:1001458 + spectrum generation information + + + + + Vocabularies describing the spectrum generation information. + PSI:PI + + + + + + + + + + + + + + Format of data files. + MS + MS:1001459 + file format + + + + + Format of data files. + PSI:MS + + + + + + + + + This term should be given if the modification was unknown. + MS + MS:1001460 + unknown modification + + + + + This term should be given if the modification was unknown. + PSI:PI + + + + + + + + + Greylag identification software. + MS + MS:1001461 + greylag + + + + + Greylag identification software. + http://greylag.org/ + + + + + + + + + The sequence database was stored in the PEFF (PSI enhanced FastA file) format. + MS + MS:1001462 + PEFF format + + + + + The sequence database was stored in the PEFF (PSI enhanced FastA file) format. + PSI:PI + + + + + + + + + + Phenyx open XML file format. + MS + MS:1001463 + Phenyx XML format + + + + + Phenyx open XML file format. + PSI:PI + + + + + + + + + DTASelect file format. + MS + MS:1001464 + DTASelect format + + + + + DTASelect file format. + PMID:12643522 + http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html + + + + + + + + + MS2 file format for MS2 spectral data. + MS + MS:1001466 + MS2 format + + + + + MS2 file format for MS2 spectral data. + DOI:10.1002/rcm.1603 + PMID:15317041 + http://fields.scripps.edu/sequest/SQTFormat.html + + + + + + + + + + + + + + + This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens. + MS + MS:1001467 + taxonomy: NCBI TaxID + + + + + This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens. + PSI:PI + + + + + + + + + + + + + + + This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. + MS + MS:1001468 + taxonomy: common name + + + + + This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. + PSI:PI + + + + + + + + + + + + + + + This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. + MS + MS:1001469 + taxonomy: scientific name + + + + + This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. + PSI:PI + + + + + + + + + + + + + + + This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. + MS + MS:1001470 + taxonomy: Swiss-Prot ID + + + + + This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible. + PSI:PI + + + + + + + + + + + + + + The children of this term can be used to describe modifications. + MS + MS:1001471 + peptide modification details + + + + + The children of this term can be used to describe modifications. + PSI:PI + + + + + + + + + Representation of an array of the measurements of a selectively monitored ion versus time. + SIM chromatogram + MS + MS:1001472 + selected ion monitoring chromatogram + + + + + Representation of an array of the measurements of a selectively monitored ion versus time. + PSI:MS + + + + + + + + + Representation of an array of the measurements of a selectively monitored reaction versus time. + SRM chromatogram + MS + MS:1001473 + selected reaction monitoring chromatogram + + + + + Representation of an array of the measurements of a selectively monitored reaction versus time. + PSI:MS + + + + + + + + + OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time. + CRM chromatogram + MS + MS:1001474 + This term was made obsolete because, by design, it can't be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way. + consecutive reaction monitoring chromatogram + true + + + + + OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time. + PSI:MS + + + + + + + + + Open Mass Spectrometry Search Algorithm was used to analyze the spectra. + MS + MS:1001475 + OMSSA + + + + + Open Mass Spectrometry Search Algorithm was used to analyze the spectra. + PSI:PI + + + + + + + + + X!Tandem was used to analyze the spectra. + MS + MS:1001476 + X!Tandem + + + + + X!Tandem was used to analyze the spectra. + PSI:PI + + + + + + + + + + Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline. + MS + MS:1001477 + SpectraST + + + + + Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline. + PSI:PI + + + + + + + + + Mascot Parser was used to analyze the spectra. + MS + MS:1001478 + Mascot Parser + + + + + Mascot Parser was used to analyze the spectra. + PSI:PI + + + + + + + + + Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte. + MS + MS:1001479 + null-terminated ASCII string + + + + + Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte. + PSI:MS + + + + + + + + + Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger. + MS + MS:1001480 + SCIEX TOF/TOF nativeID format + + + + + Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database. + MS + MS:1001481 + SCIEX TOF/TOF database + + + + + Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database. + PSI:MS + + + + + + + + + SCIEX 5800 TOF-TOF Analyzer. + MS + MS:1001482 + 5800 TOF/TOF + + + + + SCIEX 5800 TOF-TOF Analyzer. + PSI:MS + + + + + + + + + + + + SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis. + MS + MS:1001483 + SCIEX TOF/TOF Series Explorer Software + + + + + SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis. + PSI:MS + + + + + + + + + Normalization of data point intensities. + MS + MS:1001484 + intensity normalization + + + + + Normalization of data point intensities. + PSI:MS + + + + + + + + + Calibration of data point m/z positions. + MS + MS:1001485 + m/z calibration + + + + + Calibration of data point m/z positions. + PSI:MS + + + + + + + + + Filtering out part of the data. + MS + MS:1001486 + data filtering + + + + + Filtering out part of the data. + PSI:MS + + + + + + + + + + An algorithm for protein determination/assembly integrated into Bruker's ProteinScape. + MS + MS:1001487 + ProteinExtractor + + + + + An algorithm for protein determination/assembly integrated into Bruker's ProteinScape. + PSI:MS + + + + + + + + + + Mascot Distiller. + MS + MS:1001488 + Mascot Distiller + + + + + Mascot Distiller. + PSI:PI + + + + + + + + + Mascot Integra. + MS + MS:1001489 + Mascot Integra + + + + + Mascot Integra. + PSI:PI + + + + + + + + + Percolator. + MS + MS:1001490 + Percolator + + + + + Percolator. + PSI:PI + + + + + + + + + + + + + + + Percolator:Q value. + MS + MS:1001491 + percolator:Q value + + + + + Percolator:Q value. + PSI:PI + + + + + + + + + + + + + + + Percolator:score. + MS + MS:1001492 + percolator:score + + + + + Percolator:score. + PSI:PI + + + + + + + + + + + + + + + Posterior error probability. + MS + MS:1001493 + percolator:PEP + + + + + Posterior error probability. + PSI:PI + + + + + + + + + In case no threshold was used. + MS + MS:1001494 + no threshold + + + + + In case no threshold was used. + PSI:PI + + + + + + + + + + + + + + + The SearchResultId of this peptide as SearchResult in the ProteinScape database. + MS + MS:1001495 + ProteinScape:SearchResultId + + + + + The SearchResultId of this peptide as SearchResult in the ProteinScape database. + PSI:PI + + + + + + + + + + + + + + + The SearchEventId of the SearchEvent in the ProteinScape database. + MS + MS:1001496 + ProteinScape:SearchEventId + + + + + The SearchEventId of the SearchEvent in the ProteinScape database. + PSI:PI + + + + + + + + + + + + + + + The Profound probability score stored by ProteinScape. + MS + MS:1001497 + ProteinScape:ProfoundProbability + + + + + The Profound probability score stored by ProteinScape. + PSI:PI + + + + + + + + + + + + + + + The Profound z value. + MS + MS:1001498 + Profound:z value + + + + + The Profound z value. + PSI:PI + + + + + + + + + + + + + + + The Profound cluster score. + MS + MS:1001499 + Profound:Cluster + + + + + The Profound cluster score. + PSI:PI + + + + + + + + + + + + + + + The Profound cluster rank. + MS + MS:1001500 + Profound:ClusterRank + + + + + The Profound cluster rank. + PSI:PI + + + + + + + + + + + + + + + The MSFit Mowse score. + MS + MS:1001501 + MSFit:Mowse score + + + + + The MSFit Mowse score. + PSI:PI + + + + + + + + + + + + + + + The Sonar score. + MS + MS:1001502 + Sonar:Score + + + + + The Sonar score. + PSI:PI + + + + + + + + + + + + + + + The ProteinSolver exp value stored by ProteinScape. + MS + MS:1001503 + ProteinScape:PFFSolverExp + + + + + The ProteinSolver exp value stored by ProteinScape. + PSI:PI + + + + + + + + + + + + + + + The ProteinSolver score stored by ProteinScape. + MS + MS:1001504 + ProteinScape:PFFSolverScore + + + + + The ProteinSolver score stored by ProteinScape. + PSI:PI + + + + + + + + + + + + + + + The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape. + MS + MS:1001505 + ProteinScape:IntensityCoverage + + + + + The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores. + MS + MS:1001506 + ProteinScape:SequestMetaScore + + + + + The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores. + PSI:PI + + + + + + + + + + + + + + + The score calculated by ProteinExtractor. + MS + MS:1001507 + ProteinExtractor:Score + + + + + The score calculated by ProteinExtractor. + PSI:PI + + + + + + + + + Native format defined by scanId=xsd:nonNegativeInteger. + MS + MS:1001508 + Agilent MassHunter nativeID format + + + + + Native format defined by scanId=xsd:nonNegativeInteger. + PSI:PI + + + + + + + + + A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer. + MS + MS:1001509 + Agilent MassHunter format + + + + + A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer. + PSI:PI + + + + + + + + + TSQ Vantage. + MS + MS:1001510 + TSQ Vantage + + + + + TSQ Vantage. + PSI:MS + + + + + + + + + Filter types which are used to filter a sequence database. + MS + MS:1001511 + Sequence database filter types + + + + + Filter types which are used to filter a sequence database. + PSI:PI + + + + + + + + + Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search. + MS + MS:1001512 + Sequence database filters + + + + + Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search. + PSI:PI + + + + + + + + + + + + + + + DB sequence filter pattern. + MS + MS:1001513 + DB sequence filter pattern + + + + + DB sequence filter pattern. + PSI:MS + + + + + + + + + + + + + + + DB accession filter string. + MS + MS:1001514 + DB accession filter string + + + + + DB accession filter string. + PSI:MS + + + + + + + + + Fragmentation information, type of product: c ion without water. + MS + MS:1001515 + frag: c ion - H2O + + + + + Fragmentation information, type of product: c ion without water. + PSI:PI + + + + + + + + + Fragmentation information, type of product: c ion without ammonia. + MS + MS:1001516 + frag: c ion - NH3 + + + + + Fragmentation information, type of product: c ion without ammonia. + PSI:PI + + + + + + + + + Fragmentation information, type of product: z ion without water. + MS + MS:1001517 + frag: z ion - H2O + + + + + Fragmentation information, type of product: z ion without water. + PSI:PI + + + + + + + + + Fragmentation information, type of product: z ion without ammonia. + MS + MS:1001518 + frag: z ion - NH3 + + + + + Fragmentation information, type of product: z ion without ammonia. + PSI:PI + + + + + + + + + Fragmentation information, type of product: x ion without water. + MS + MS:1001519 + frag: x ion - H2O + + + + + Fragmentation information, type of product: x ion without water. + PSI:PI + + + + + + + + + Fragmentation information, type of product: x ion without ammonia. + MS + MS:1001520 + frag: x ion - NH3 + + + + + Fragmentation information, type of product: x ion without ammonia. + PSI:PI + + + + + + + + + Fragmentation information, type of product: precursor ion without water. + MS + MS:1001521 + frag: precursor ion - H2O + + + + + Fragmentation information, type of product: precursor ion without water. + PSI:PI + + + + + + + + + Fragmentation information, type of product: precursor ion without ammonia. + MS + MS:1001522 + frag: precursor ion - NH3 + + + + + Fragmentation information, type of product: precursor ion without ammonia. + PSI:PI + + + + + + + + + Fragmentation information, type of product: precursor ion. + MS + MS:1001523 + frag: precursor ion + + + + + Fragmentation information, type of product: precursor ion. + PSI:PI + + + + + + + + + + + + + + + + + + + + + This term can describe a neutral loss m/z value that is lost from an ion. + MS + MS:1001524 + fragment neutral loss + + + + + This term can describe a neutral loss m/z value that is lost from an ion. + PSI:PI + + + + + + + + + + + + + + + + + + + + + This term can describe a neutral loss m/z value that is lost from an ion. + MS + MS:1001525 + precursor neutral loss + + + + + This term can describe a neutral loss m/z value that is lost from an ion. + PSI:PI + + + + + + + + + Native format defined by databasekey=xsd:long. + MS + MS:1001526 + A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). + spectrum from database integer nativeID format + + + + + Native format defined by databasekey=xsd:long. + PSI:MS + + + + + + + + + Spectra from Bruker/Protagen Proteinscape database. + MS + MS:1001527 + Proteinscape spectra + + + + + Spectra from Bruker/Protagen Proteinscape database. + PSI:MS + + + + + + + + + + Native format defined by query=xsd:nonNegativeInteger. + MS + MS:1001528 + The spectrum (query) number in a Mascot results file, starting from 1. + Mascot query number + + + + + Native format defined by query=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + Child-terms contain information to map the results back to spectra. + MS + MS:1001529 + spectra data details + + + + + Child-terms contain information to map the results back to spectra. + PSI:MS + + + + + + + + + Native format defined by mzMLid=xsd:IDREF. + MS + MS:1001530 + A unique identifier of a spectrum stored in an mzML file. + mzML unique identifier + + + + + Native format defined by mzMLid=xsd:IDREF. + PSI:MS + + + + + + + + + + Native format defined by databasekey=xsd:long. + MS + MS:1001531 + A unique identifier of a spectrum stored in a ProteinScape database. + spectrum from ProteinScape database nativeID format + + + + + Native format defined by databasekey=xsd:long. + PSI:MS + + + + + + + + + + Native format defined by databasekey=xsd:string. + MS + MS:1001532 + A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). + spectrum from database string nativeID format + + + + + Native format defined by databasekey=xsd:string. + PSI:MS + + + + + + + + + Bruker Daltonics' esquire series. + MS + MS:1001533 + Bruker Daltonics esquire series + + + + + Bruker Daltonics' esquire series. + PSI:MS + + + + + + + + + Bruker Daltonics' flex series. + MS + MS:1001534 + Bruker Daltonics flex series + + + + + Bruker Daltonics' flex series. + PSI:MS + + + + + + + + + Bruker Daltonics' BioTOF series. + MS + MS:1001535 + Bruker Daltonics BioTOF series + + + + + Bruker Daltonics' BioTOF series. + PSI:MS + + + + + + + + + Bruker Daltonics' micrOTOF series. + MS + MS:1001536 + Bruker Daltonics micrOTOF series + + + + + Bruker Daltonics' micrOTOF series. + PSI:MS + + + + + + + + + Bruker Daltonics' BioTOF: ESI TOF. + MS + MS:1001537 + BioTOF + + + + + Bruker Daltonics' BioTOF: ESI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' BioTOF III: ESI TOF. + MS + MS:1001538 + BioTOF III + + + + + Bruker Daltonics' BioTOF III: ESI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional). + MS + MS:1001539 + UltroTOF-Q + + + + + Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional). + PSI:MS + + + + + + + + + Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI. + MS + MS:1001540 + micrOTOF II + + + + + Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI. + MS + MS:1001541 + maXis + + + + + Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI. + PSI:MS + + + + + + + + + Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR. + MS + MS:1001542 + amaZon ETD + + + + + Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR. + PSI:MS + + + + + + + + + Bruker Daltonics' microflex LRF: MALDI TOF. + MS + MS:1001543 + microflex LRF + + + + + Bruker Daltonics' microflex LRF: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' ultrafleXtreme: MALDI TOF. + MS + MS:1001544 + ultrafleXtreme + + + + + Bruker Daltonics' ultrafleXtreme: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' amaZon series. + MS + MS:1001545 + Bruker Daltonics amaZon series + + + + + Bruker Daltonics' amaZon series. + PSI:MS + + + + + + + + + Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. + MS + MS:1001546 + amaZon X + + + + + Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. + PSI:MS + + + + + + + + + Bruker Daltonics' maXis series. + MS + MS:1001547 + Bruker Daltonics maXis series + + + + + Bruker Daltonics' maXis series. + PSI:MS + + + + + + + + + Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. + MS + MS:1001548 + Bruker Daltonics solarix series + + + + + Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR. + PSI:MS + + + + + + + + + Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR. + MS + MS:1001549 + solariX + + + + + Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR. + PSI:MS + + + + + + + + + Bruker Daltonics' microflex II: MALDI TOF. + MS + MS:1001550 + microflex II + + + + + Bruker Daltonics' microflex II: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF. + MS + MS:1001553 + autoflex II TOF/TOF + + + + + Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF. + MS + MS:1001554 + autoflex III TOF/TOF smartbeam + + + + + Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' autoflex: MALDI TOF. + MS + MS:1001555 + autoflex + + + + + Bruker Daltonics' autoflex: MALDI TOF. + PSI:MS + + + + + + + + + Bruker Daltonics' apex series. + MS + MS:1001556 + Bruker Daltonics apex series + + + + + Bruker Daltonics' apex series. + PSI:MS + + + + + + + + + Shimadzu Corporation software. + MS + MS:1001557 + Shimadzu Corporation software + + + + + Shimadzu Corporation software. + PSI:MS + + + + + + + + + + + + Shimadzu Biotech software for data acquisition, processing, and analysis. + MS + MS:1001558 + MALDI Solutions + + + + + Shimadzu Biotech software for data acquisition, processing, and analysis. + PSI:MS + + + + + + + + + Native format defined by file=xsd:IDREF. + MS + MS:1001559 + SCIEX TOF/TOF T2D nativeID format + + + + + Native format defined by file=xsd:IDREF. + PSI:MS + + + + + + + + + Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format. + MS + MS:1001560 + SCIEX TOF/TOF T2D format + + + + + Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format. + PSI:MS + + + + + + + + + Scaffold analysis software. + MS + MS:1001561 + Scaffold + + + + + Scaffold analysis software. + http://www.proteomesoftware.com + + + + + + + + + Scaffold native ID format. + MS + MS:1001562 + Scaffold nativeID format + + + + + Scaffold native ID format. + PSI:MS + + + + + + + + + Source file for this mzIdentML was in SEQUEST SQT format. + MS + MS:1001563 + SEQUEST SQT format + + + + + Source file for this mzIdentML was in SEQUEST SQT format. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format. + MS + MS:1001564 + Discoverer MSF format + + + + + Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in Waters IdentityE XML format. + MS + MS:1001565 + IdentityE XML format + + + + + Source file for this mzIdentML was in Waters IdentityE XML format. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in Waters ProteinLynx XML format. + MS + MS:1001566 + ProteinLynx XML format + + + + + Source file for this mzIdentML was in Waters ProteinLynx XML format. + PSI:PI + + + + + + + + + Source file for this mzIdentML was in Agilent SpectrumMill directory format. + MS + MS:1001567 + SpectrumMill directories + + + + + Source file for this mzIdentML was in Agilent SpectrumMill directory format. + PSI:PI + + + + + + + + + + + + + + + Scaffold peptide probability score. + MS + MS:1001568 + Scaffold:Peptide Probability + + + + + Scaffold peptide probability score. + PSI:PI + + + + + + + + + + + + + + + Waters IdentityE peptide score. + MS + MS:1001569 + IdentityE Score + + + + + Waters IdentityE peptide score. + PSI:PI + + + + + + + + + + + + + + + ProteinLynx log likelihood score. + MS + MS:1001570 + ProteinLynx:Log Likelihood + + + + + ProteinLynx log likelihood score. + PSI:PI + + + + + + + + + + + + + + + Waters ProteinLynx Ladder score. + MS + MS:1001571 + ProteinLynx:Ladder Score + + + + + Waters ProteinLynx Ladder score. + PSI:PI + + + + + + + + + + + + + + + Spectrum mill peptide score. + MS + MS:1001572 + SpectrumMill:Score + + + + + Spectrum mill peptide score. + PSI:PI + + + + + + + + + + + + + + + SpectrumMill SPI score (%). + MS + MS:1001573 + SpectrumMill:SPI + + + + + SpectrumMill SPI score (%). + PSI:PI + + + + + + + + + Flag indicating to report only the spectra assigned to identified proteins. + MS + MS:1001574 + report only spectra assigned to identified proteins + + + + + Flag indicating to report only the spectra assigned to identified proteins. + PSI:PI + + + + + + + + + + + + + + + Minimum number of peptides a protein must have to be accepted. + MS + MS:1001575 + Scaffold: Minimum Peptide Count + + + + + Minimum number of peptides a protein must have to be accepted. + PSI:PI + + + + + + + + + + + + + + + Minimum protein probability a protein must have to be accepted. + MS + MS:1001576 + Scaffold: Minimum Protein Probability + + + + + Minimum protein probability a protein must have to be accepted. + PSI:PI + + + + + + + + + + + + + + + Minimum probability a peptide must have to be accepted for protein scoring. + MS + MS:1001577 + Scaffold: Minimum Peptide Probability + + + + + Minimum probability a peptide must have to be accepted for protein scoring. + PSI:PI + + + + + + + + + + + + + + + Minimum number of enzymatic termini a peptide must have to be accepted. + MS + MS:1001578 + minimum number of enzymatic termini + + + + + Minimum number of enzymatic termini a peptide must have to be accepted. + PSI:PI + + + + + + + + + + + + + + + Scaffold protein probability score. + MS + MS:1001579 + Scaffold:Protein Probability + + + + + Scaffold protein probability score. + PSI:PI + + + + + + + + + + + + + + + Discriminant score from Agilent SpectrumMill software. + MS + MS:1001580 + SpectrumMill:Discriminant Score + + + + + Discriminant score from Agilent SpectrumMill software. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion. + FAIMS CV + MS + MS:1001581 + FAIMS compensation voltage + + + + + The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion. + PSI:MS + + + + + + + + + + Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data. + MS + MS:1001582 + XCMS + + + + + Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data. + PSI:MS + + + + + + + + + + MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data. + MS + MS:1001583 + MaxQuant + + + + + MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data. + PSI:MS + + + + + + + + + Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF). + MS + MS:1001584 + combined pmf + ms-ms search + + + + + Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF). + PSI:MS + + + + + + + + + Tabb Lab software for directly comparing peptides in a database to tandem mass spectra. + MS + MS:1001585 + MyriMatch + + + + + Tabb Lab software for directly comparing peptides in a database to tandem mass spectra. + PSI:MS + + + + + + + + + Tabb Lab software for generating sequence tags from tandem mass spectra. + MS + MS:1001586 + DirecTag + + + + + Tabb Lab software for generating sequence tags from tandem mass spectra. + PSI:MS + + + + + + + + + Tabb Lab software for reconciling sequence tags to a protein database. + MS + MS:1001587 + TagRecon + + + + + Tabb Lab software for reconciling sequence tags to a protein database. + PSI:MS + + + + + + + + + Tabb Lab software for spectral library searches on tandem mass spectra. + MS + MS:1001588 + Pepitome + + + + + Tabb Lab software for spectral library searches on tandem mass spectra. + PSI:MS + + + + + + + + + Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance. + Pepitome:MVH + TagRecon:MVH + MS + MS:1001589 + MyriMatch:MVH + + + + + Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance. + PSI:MS + + + + + + + + + The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution. + Pepitome:mzFidelity + TagRecon:mzFidelity + MS + MS:1001590 + MyriMatch:mzFidelity + + + + + The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution. + PSI:MS + + + + + + + + + + + + + + + A representative protein selected from a set of sequence same-set or spectrum same-set proteins. + MS + MS:1001591 + anchor protein + + + + + A representative protein selected from a set of sequence same-set or spectrum same-set proteins. + PSI:MS + + + + + + + + + + + + + + + A protein with significant homology to another protein, but some distinguishing peptide matches. + MS + MS:1001592 + family member protein + + + + + A protein with significant homology to another protein, but some distinguishing peptide matches. + PSI:MS + + + + + + + + + TO ENDETAIL: a really generic relationship OR ortholog protein. + MS + MS:1001593 + group member with undefined relationship OR ortholog protein + + + + + TO ENDETAIL: a really generic relationship OR ortholog protein. + PSI:MS + + + + + + + + + + + + + + + A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences. + MS + MS:1001594 + sequence same-set protein + + + + + A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences. + PSI:MS + + + + + + + + + + + + + + + A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra. + MS + MS:1001595 + spectrum same-set protein + + + + + A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra. + PSI:MS + + + + + + + + + + + + + + + A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches. + MS + MS:1001596 + sequence sub-set protein + + + + + A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches. + PSI:MS + + + + + + + + + + + + + + + A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches. + MS + MS:1001597 + spectrum sub-set protein + + + + + A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches. + PSI:MS + + + + + + + + + + + + + + + A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins. + MS + MS:1001598 + sequence subsumable protein + + + + + A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins. + PSI:MS + + + + + + + + + + + + + + + A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins. + MS + MS:1001599 + spectrum subsumable protein + + + + + A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins. + PSI:MS + + + + + + + + + + + + + + + Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable). + MS + MS:1001600 + protein inference confidence category + + + + + Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable). + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Name and location of the .raw file or files. + MS + MS:1001601 + This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. + ProteomeDiscoverer:Spectrum Files:Raw File names + true + + + + + OBSOLETE Name and location of the .raw file or files. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Path and name of the .srf (SEQUEST Result Format) file. + MS + MS:1001602 + This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. + ProteomeDiscoverer:SRF File Selector:SRF File Path + true + + + + + OBSOLETE Path and name of the .srf (SEQUEST Result Format) file. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc). + MS + MS:1001603 + This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead. + ProteomeDiscoverer:Spectrum Selector:Ionization Source + true + + + + + OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc). + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any). + MS + MS:1001604 + This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead. + ProteomeDiscoverer:Activation Type + true + + + + + OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any). + PSI:MS + + + + + + + + + + + + + + + Lower retention-time limit. + MS + MS:1001605 + ProteomeDiscoverer:Spectrum Selector:Lower RT Limit + + + + + Lower retention-time limit. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS). + MS + MS:1001606 + This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead. + ProteomeDiscoverer:Mass Analyzer + true + + + + + OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS). + PSI:MS + + + + + + + + + + + + + + + Maximum mass limit of a singly charged precursor ion. + MS + MS:1001607 + ProteomeDiscoverer:Max Precursor Mass + + + + + Maximum mass limit of a singly charged precursor ion. + PSI:MS + + + + + + + + + + + + + + + Minimum mass limit of a singly charged precursor ion. + MS + MS:1001608 + ProteomeDiscoverer:Min Precursor Mass + + + + + Minimum mass limit of a singly charged precursor ion. + PSI:MS + + + + + + + + + + + + + + + Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow. + MS + MS:1001609 + ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count + + + + + Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Level of the mass spectrum (MS2 ... MS10). + MS + MS:1001610 + This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead. + ProteomeDiscoverer:MS Order + true + + + + + OBSOLETE Level of the mass spectrum (MS2 ... MS10). + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Polarity mode (positive or negative). + MS + MS:1001611 + This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead. + ProteomeDiscoverer:Polarity Mode + true + + + + + OBSOLETE Polarity mode (positive or negative). + PSI:MS + + + + + + + + + + + + + + + Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3). + MS + MS:1001612 + ProteomeDiscoverer:Spectrum Selector:Precursor Selection + + + + + Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3). + PSI:MS + + + + + + + + + + + + + + + Signal-to-Noise ratio below which peaks are removed. + MS + MS:1001613 + ProteomeDiscoverer:SN Threshold + + + + + Signal-to-Noise ratio below which peaks are removed. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)). + MS + MS:1001614 + This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead. + ProteomeDiscoverer:Scan Type + true + + + + + OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)). + PSI:MS + + + + + + + + + + + + + + + Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value. + MS + MS:1001615 + ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold + + + + + Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value. + PSI:MS + + + + + + + + + + + + + + + Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header. + MS + MS:1001616 + ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements + + + + + Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header. + PSI:MS + + + + + + + + + + + + + + + Specifies the charge state of the precursor ions, if it is not defined in the scan header. + MS + MS:1001617 + ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements + + + + + Specifies the charge state of the precursor ions, if it is not defined in the scan header. + PSI:MS + + + + + + + + + + + + + + + Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header. + MS + MS:1001618 + ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements + + + + + Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header. + PSI:MS + + + + + + + + + + + + + + + Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header. + MS + MS:1001619 + ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements + + + + + Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header. + PSI:MS + + + + + + + + + + + + + + + Specifies the polarity of the ions monitored if it is not included in the scan header. + MS + MS:1001620 + ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements + + + + + Specifies the polarity of the ions monitored if it is not included in the scan header. + PSI:MS + + + + + + + + + + + + + + + Upper retention-time limit. + MS + MS:1001621 + ProteomeDiscoverer:Spectrum Selector:Upper RT Limit + + + + + Upper retention-time limit. + PSI:MS + + + + + + + + + + + + + + + Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors. + MS + MS:1001622 + ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset + + + + + Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors. + PSI:MS + + + + + + + + + + + + + + + Maximum allowed mass of a neutral loss. + MS + MS:1001623 + ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass + + + + + Maximum allowed mass of a neutral loss. + PSI:MS + + + + + + + + + + + + + + + Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed. + MS + MS:1001624 + ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor + + + + + Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed. + PSI:MS + + + + + + + + + + + + + + + Determines whether neutral loss peaks are removed from ETD and ECD spectra. + MS + MS:1001625 + ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks + + + + + Determines whether neutral loss peaks are removed from ETD and ECD spectra. + PSI:MS + + + + + + + + + + + + + + + Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra. + MS + MS:1001626 + ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses + + + + + Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra. + PSI:MS + + + + + + + + + + + + + + + Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum. + MS + MS:1001627 + ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones + + + + + Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum. + PSI:MS + + + + + + + + + + + + + + + Determines whether precursor artifact peaks from the MS2 input spectra are removed. + MS + MS:1001628 + ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak + + + + + Determines whether precursor artifact peaks from the MS2 input spectra are removed. + PSI:MS + + + + + + + + + + + + + + + Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type. + MS + MS:1001629 + ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch + + + + + Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type. + PSI:MS + + + + + + + + + + + + + + + Determines whether spectra from different MS order scans can be grouped together. + MS + MS:1001630 + ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch + + + + + Determines whether spectra from different MS order scans can be grouped together. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species. + MS + MS:1001631 + This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead. + ProteomeDiscoverer:Spectrum Grouper:Max RT Difference + true + + + + + OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species. + PSI:MS + + + + + + + + + + + + + + + Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis. + MS + MS:1001632 + ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion + + + + + Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis. + PSI:MS + + + + + + + + + + + + + + + Highest charge state that is allowed for the deconvolution of multiply charged data. + MS + MS:1001633 + ProteomeDiscoverer:Xtract:Highest Charge + + + + + Highest charge state that is allowed for the deconvolution of multiply charged data. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. + MS + MS:1001634 + This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead. + ProteomeDiscoverer:Xtract:Highest MZ + true + + + + + OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. + PSI:MS + + + + + + + + + + + + + + + Lowest charge state that is allowed for the deconvolution of multiply charged data. + MS + MS:1001635 + ProteomeDiscoverer:Xtract:Lowest Charge + + + + + Lowest charge state that is allowed for the deconvolution of multiply charged data. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. + MS + MS:1001636 + This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead. + ProteomeDiscoverer:Xtract:Lowest MZ + true + + + + + OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract. + PSI:MS + + + + + + + + + + + + + + + Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum. + MS + MS:1001637 + ProteomeDiscoverer:Xtract:Monoisotopic Mass Only + + + + + Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum. + PSI:MS + + + + + + + + + + + + + + + Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted). + MS + MS:1001638 + ProteomeDiscoverer:Xtract:Overlapping Remainder + + + + + Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted). + PSI:MS + + + + + + + + + + + + + + + Accuracy required for a pattern fit to be considered valid. + MS + MS:1001639 + ProteomeDiscoverer:Xtract:Required Fitting Accuracy + + + + + Accuracy required for a pattern fit to be considered valid. + PSI:MS + + + + + + + + + + + + + + + Resolution at mass 400. + MS + MS:1001640 + ProteomeDiscoverer:Xtract:Resolution At 400 + + + + + Resolution at mass 400. + PSI:MS + + + + + + + + + + + + + + + Minimum charge state below which peptides are filtered out. + MS + MS:1001641 + ProteomeDiscoverer:Lowest Charge State + + + + + Minimum charge state below which peptides are filtered out. + PSI:MS + + + + + + + + + + + + + + + Maximum charge above which peptides are filtered out. + MS + MS:1001642 + ProteomeDiscoverer:Highest Charge State + + + + + Maximum charge above which peptides are filtered out. + PSI:MS + + + + + + + + + + + + + + + Determines whether spectra with scores above the threshold score are retained rather than filtered out. + MS + MS:1001643 + ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores + + + + + Determines whether spectra with scores above the threshold score are retained rather than filtered out. + PSI:MS + + + + + + + + + + + + + + + Determine dynamic post-translational modifications (PTMs). + MS + MS:1001644 + ProteomeDiscoverer:Dynamic Modification + + + + + Determine dynamic post-translational modifications (PTMs). + PSI:MS + + + + + + + + + + + + + + + Static Modification to all occurrences of a named amino acid. + MS + MS:1001645 + ProteomeDiscoverer:Static Modification + + + + + Static Modification to all occurrences of a named amino acid. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database. + MS + MS:1001646 + This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. + ProteomeDiscoverer:Mascot:Decoy Search + true + + + + + OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database. + PSI:MS + + + + + + + + + + + + + + + Determines whether to search error-tolerant. + MS + MS:1001647 + ProteomeDiscoverer:Mascot:Error tolerant Search + + + + + Determines whether to search error-tolerant. + PSI:MS + + + + + + + + + + + + + + + Maximum size of the .mgf (Mascot Generic Format) file in MByte. + MS + MS:1001648 + ProteomeDiscoverer:Mascot:Max MGF File Size + + + + + Maximum size of the .mgf (Mascot Generic Format) file in MByte. + PSI:MS + + + + + + + + + + + + + + + URL (Uniform resource Locator) of the Mascot server. + MS + MS:1001649 + ProteomeDiscoverer:Mascot:Mascot Server URL + + + + + URL (Uniform resource Locator) of the Mascot server. + PSI:MS + + + + + + + + + + + + + + + Number of attempts to submit the Mascot search. + MS + MS:1001650 + ProteomeDiscoverer:Mascot:Number of attempts to submit the search + + + + + Number of attempts to submit the Mascot search. + PSI:MS + + + + + + + + + + + + + + + Number of attempts to submit the Mascot search. + MS + MS:1001651 + ProteomeDiscoverer:Mascot:X Static Modification + + + + + Number of attempts to submit the Mascot search. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Name of the user submitting the Mascot search. + MS + MS:1001652 + This term was made obsolete because it's recommended to use researcher (MS:1001271) instead. + ProteomeDiscoverer:Mascot:User Name + true + + + + + OBSOLETE Name of the user submitting the Mascot search. + PSI:MS + + + + + + + + + + + + + + + Time interval between attempts to submit a search in seconds. + MS + MS:1001653 + ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search + + + + + Time interval between attempts to submit a search in seconds. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Specifies the enzyme reagent used for protein digestion. + MS + MS:1001654 + This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead. + ProteomeDiscoverer:Enzyme Name + true + + + + + OBSOLETE Specifies the enzyme reagent used for protein digestion. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu. + MS + MS:1001655 + This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. + ProteomeDiscoverer:Fragment Mass Tolerance + true + + + + + OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu. + PSI:MS + + + + + + + + + + + + + + + Type of instrument used to acquire the data in the raw file. + MS + MS:1001656 + Mascot:Instrument + + + + + Type of instrument used to acquire the data in the raw file. + PSI:MS + + + + + + + + + + + + + + + Maximum number of missed cleavage sites to consider during the digest. + MS + MS:1001657 + ProteomeDiscoverer:Maximum Missed Cleavage Sites + + + + + Maximum number of missed cleavage sites to consider during the digest. + PSI:MS + + + + + + + + + + + + + + + Minimum score in the IonScore column that each peptide must exceed in order to be reported. + MS + MS:1001658 + ProteomeDiscoverer:Mascot:Peptide CutOff Score + + + + + Minimum score in the IonScore column that each peptide must exceed in order to be reported. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Mass window for which precursor ions are considered to be the same species. + MS + MS:1001659 + This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. + ProteomeDiscoverer:Precursor Mass Tolerance + true + + + + + OBSOLETE Mass window for which precursor ions are considered to be the same species. + PSI:MS + + + + + + + + + + + + + + + Minimum protein score in the IonScore column that each protein must exceed in order to be reported. + MS + MS:1001660 + ProteomeDiscoverer:Mascot:Protein CutOff Score + + + + + Minimum protein score in the IonScore column that each protein must exceed in order to be reported. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Database to use in the search (configured on the Mascot server). + MS + MS:1001661 + This term was made obsolete because it's recommended to use database name (MS:1001013) instead. + ProteomeDiscoverer:Protein Database + true + + + + + OBSOLETE Database to use in the search (configured on the Mascot server). + PSI:MS + + + + + + + + + + + + + + + Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report. + MS + MS:1001662 + ProteomeDiscoverer:Mascot:Protein Relevance Factor + + + + + Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report. + PSI:MS + + + + + + + + + + + + + + + Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence. + MS + MS:1001663 + ProteomeDiscoverer:Target FDR Relaxed + + + + + Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence. + PSI:MS + + + + + + + + + + + + + + + Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence. + MS + MS:1001664 + ProteomeDiscoverer:Target FDR Strict + + + + + Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Limits searches to entries from a particular species or group of species. + MS + MS:1001665 + This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. + ProteomeDiscoverer:Mascot:Taxonomy + true + + + + + OBSOLETE Limits searches to entries from a particular species or group of species. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Use average mass for the precursor. + MS + MS:1001666 + This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead. + ProteomeDiscoverer:Use Average Precursor Mass + true + + + + + OBSOLETE Use average mass for the precursor. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Determines whether to use MudPIT or normal scoring. + MS + MS:1001667 + This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead. + Mascot:use MudPIT scoring + true + + + + + OBSOLETE Determines whether to use MudPIT or normal scoring. + PSI:MS + + + + + + + + + + + + + + + Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported. + MS + MS:1001668 + ProteomeDiscoverer:Absolute XCorr Threshold + + + + + Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported. + PSI:MS + + + + + + + + + + + + + + + Determines whether to calculate a probability score for every peptide match. + MS + MS:1001669 + ProteomeDiscoverer:SEQUEST:Calculate Probability Score + + + + + Determines whether to calculate a probability score for every peptide match. + PSI:MS + + + + + + + + + + + + + + + Dynamic C-terminal modification that is used during the search. + MS + MS:1001670 + ProteomeDiscoverer:SEQUEST:CTerminal Modification + + + + + Dynamic C-terminal modification that is used during the search. + PSI:MS + + + + + + + + + + + + + + + Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained. + MS + MS:1001671 + ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage + + + + + Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained. + PSI:MS + + + + + + + + + + + + + + + Maximum number of identical modifications that a single peptide can have. + MS + MS:1001672 + ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide + + + + + Maximum number of identical modifications that a single peptide can have. + PSI:MS + + + + + + + + + + + + + + + Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance. + MS + MS:1001673 + ProteomeDiscoverer:Max Modifications Per Peptide + + + + + Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance. + PSI:MS + + + + + + + + + + + + + + + Maximum number of peptides that are searched and scored per spectrum. + MS + MS:1001674 + ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered + + + + + Maximum number of peptides that are searched and scored per spectrum. + PSI:MS + + + + + + + + + + + + + + + Maximum number of peptide matches reported per spectrum. + MS + MS:1001675 + ProteomeDiscoverer:Maximum Peptides Output + + + + + Maximum number of peptide matches reported per spectrum. + PSI:MS + + + + + + + + + + + + + + + Maximum number of proteins that a single identified peptide can be associated with during protein assembly. + MS + MS:1001676 + ProteomeDiscoverer:Maximum Protein References Per Peptide + + + + + Maximum number of proteins that a single identified peptide can be associated with during protein assembly. + PSI:MS + + + + + + + + + + + + + + + Dynamic N-terminal modification that is used during the search. + MS + MS:1001677 + ProteomeDiscoverer:SEQUEST:NTerminal Modification + + + + + Dynamic N-terminal modification that is used during the search. + PSI:MS + + + + + + + + + + + + + + + Static modification for the C terminal of the peptide used during the search. + MS + MS:1001678 + ProteomeDiscoverer:Peptide CTerminus + + + + + Static modification for the C terminal of the peptide used during the search. + PSI:MS + + + + + + + + + + + + + + + Static modification for the N terminal of the peptide used during the search. + MS + MS:1001679 + ProteomeDiscoverer:Peptide NTerminus + + + + + Static modification for the N terminal of the peptide used during the search. + PSI:MS + + + + + + + + + + + + + + + Specifies a factor to apply to the protein score. + MS + MS:1001680 + ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor + + + + + Specifies a factor to apply to the protein score. + PSI:MS + + + + + + + + + + + + + + + Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report. + MS + MS:1001681 + ProteomeDiscoverer:Protein Relevance Threshold + + + + + Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database. + MS + MS:1001682 + This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. + ProteomeDiscoverer:Search Against Decoy Database + true + + + + + OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database. + PSI:MS + + + + + + + + + + + + + + + Use average masses for the fragments. + MS + MS:1001683 + ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses + + + + + Use average masses for the fragments. + PSI:MS + + + + + + + + + + + + + + + Determines whether a ions with neutral loss are used for spectrum matching. + MS + MS:1001684 + ProteomeDiscoverer:Use Neutral Loss a Ions + + + + + Determines whether a ions with neutral loss are used for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines whether b ions with neutral loss are used for spectrum matching. + MS + MS:1001685 + ProteomeDiscoverer:Use Neutral Loss b Ions + + + + + Determines whether b ions with neutral loss are used for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines whether y ions with neutral loss are used for spectrum matching. + MS + MS:1001686 + ProteomeDiscoverer:Use Neutral Loss y Ions + + + + + Determines whether y ions with neutral loss are used for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines whether z ions with neutral loss are used for spectrum matching. + MS + MS:1001687 + ProteomeDiscoverer:Use Neutral Loss z Ions + + + + + Determines whether z ions with neutral loss are used for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Uses a ions for spectrum matching with this relative factor. + MS + MS:1001688 + ProteomeDiscoverer:SEQUEST:Weight of a Ions + + + + + Uses a ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Uses b ions for spectrum matching with this relative factor. + MS + MS:1001689 + ProteomeDiscoverer:SEQUEST:Weight of b Ions + + + + + Uses b ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Uses c ions for spectrum matching with this relative factor. + MS + MS:1001690 + ProteomeDiscoverer:SEQUEST:Weight of c Ions + + + + + Uses c ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Uses c ions for spectrum matching with this relative factor. + MS + MS:1001691 + ProteomeDiscoverer:SEQUEST:Weight of d Ions + + + + + Uses c ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Uses c ions for spectrum matching with this relative factor. + MS + MS:1001692 + ProteomeDiscoverer:SEQUEST:Weight of v Ions + + + + + Uses c ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Uses c ions for spectrum matching with this relative factor. + MS + MS:1001693 + ProteomeDiscoverer:SEQUEST:Weight of w Ions + + + + + Uses c ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Uses x ions for spectrum matching with this relative factor. + MS + MS:1001694 + ProteomeDiscoverer:SEQUEST:Weight of x Ions + + + + + Uses x ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Uses y ions for spectrum matching with this relative factor. + MS + MS:1001695 + ProteomeDiscoverer:SEQUEST:Weight of y Ions + + + + + Uses y ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Uses z ions for spectrum matching with this relative factor. + MS + MS:1001696 + ProteomeDiscoverer:SEQUEST:Weight of z Ions + + + + + Uses z ions for spectrum matching with this relative factor. + PSI:MS + + + + + + + + + + + + + + + Sets a minimum protein score that each protein must exceed in order to be reported. + MS + MS:1001697 + ProteomeDiscoverer:ZCore:Protein Score Cutoff + + + + + Sets a minimum protein score that each protein must exceed in order to be reported. + PSI:MS + + + + + + + + + + + + + + + Specifies which peak to select if more than one peak is found inside the integration window. + MS + MS:1001698 + ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method + + + + + Specifies which peak to select if more than one peak is found inside the integration window. + PSI:MS + + + + + + + + + + + + + + + Specifies the mass-to-charge window that enables one to look for the reporter peaks. + MS + MS:1001699 + ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance + + + + + Specifies the mass-to-charge window that enables one to look for the reporter peaks. + PSI:MS + + + + + + + + + + + + + + + Quantitation method for isobarically labeled quantitation. + MS + MS:1001700 + ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method + + + + + Quantitation method for isobarically labeled quantitation. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Format of the exported spectra (dta, mgf or mzData). + MS + MS:1001701 + This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. + ProteomeDiscoverer:Spectrum Exporter:Export Format + true + + + + + OBSOLETE Format of the exported spectra (dta, mgf or mzData). + PSI:MS + + + + + + + + + + + + + + + Name of the output file that contains the exported data. + MS + MS:1001702 + ProteomeDiscoverer:Spectrum Exporter:File name + + + + + Name of the output file that contains the exported data. + PSI:MS + + + + + + + + + + + + + + + Influences the modifications search. + MS + MS:1001703 + ProteomeDiscoverer:Search Modifications Only For Identified Proteins + + + + + Influences the modifications search. + PSI:MS + + + + + + + + + + + + + + + Standard high confidence XCorr parameter for charge = 1. + MS + MS:1001704 + ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1 + + + + + Standard high confidence XCorr parameter for charge = 1. + PSI:MS + + + + + + + + + + + + + + + Standard high confidence XCorr parameter for charge = 2. + MS + MS:1001705 + ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2 + + + + + Standard high confidence XCorr parameter for charge = 2. + PSI:MS + + + + + + + + + + + + + + + Standard high confidence XCorr parameter for charge = 3. + MS + MS:1001706 + ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3 + + + + + Standard high confidence XCorr parameter for charge = 3. + PSI:MS + + + + + + + + + + + + + + + Standard high confidence XCorr parameter for charge >= 4. + MS + MS:1001707 + ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4 + + + + + Standard high confidence XCorr parameter for charge >= 4. + PSI:MS + + + + + + + + + + + + + + + Standard medium confidence XCorr parameter for charge = 1. + MS + MS:1001708 + ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1 + + + + + Standard medium confidence XCorr parameter for charge = 1. + PSI:MS + + + + + + + + + + + + + + + Standard medium confidence XCorr parameter for charge = 2. + MS + MS:1001709 + ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2 + + + + + Standard medium confidence XCorr parameter for charge = 2. + PSI:MS + + + + + + + + + + + + + + + Standard medium confidence XCorr parameter for charge = 3. + MS + MS:1001710 + ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3 + + + + + Standard medium confidence XCorr parameter for charge = 3. + PSI:MS + + + + + + + + + + + + + + + Standard medium confidence XCorr parameter for charge >= 4. + MS + MS:1001711 + ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4 + + + + + Standard medium confidence XCorr parameter for charge >= 4. + PSI:MS + + + + + + + + + + + + + + + FT high confidence XCorr parameter for charge = 1. + MS + MS:1001712 + ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1 + + + + + FT high confidence XCorr parameter for charge = 1. + PSI:MS + + + + + + + + + + + + + + + FT high confidence XCorr parameter for charge = 2. + MS + MS:1001713 + ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2 + + + + + FT high confidence XCorr parameter for charge = 2. + PSI:MS + + + + + + + + + + + + + + + FT high confidence XCorr parameter for charge = 3. + MS + MS:1001714 + ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3 + + + + + FT high confidence XCorr parameter for charge = 3. + PSI:MS + + + + + + + + + + + + + + + FT high confidence XCorr parameter for charge >= 4. + MS + MS:1001715 + ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4 + + + + + FT high confidence XCorr parameter for charge >= 4. + PSI:MS + + + + + + + + + + + + + + + FT medium confidence XCorr parameter for charge = 1. + MS + MS:1001716 + ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1 + + + + + FT medium confidence XCorr parameter for charge = 1. + PSI:MS + + + + + + + + + + + + + + + FT medium confidence XCorr parameter for charge = 2. + MS + MS:1001717 + ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2 + + + + + FT medium confidence XCorr parameter for charge = 2. + PSI:MS + + + + + + + + + + + + + + + FT medium confidence XCorr parameter for charge = 3. + MS + MS:1001718 + ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3 + + + + + FT medium confidence XCorr parameter for charge = 3. + PSI:MS + + + + + + + + + + + + + + + FT medium confidence XCorr parameter for charge >= 4. + MS + MS:1001719 + ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4 + + + + + FT medium confidence XCorr parameter for charge >= 4. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter. + MS + MS:1001720 + This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. + ProteomeDiscoverer:1. Dynamic Modification + true + + + + + OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter. + MS + MS:1001721 + This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. + ProteomeDiscoverer:2. Dynamic Modification + true + + + + + OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter. + MS + MS:1001722 + This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. + ProteomeDiscoverer:3. Dynamic Modification + true + + + + + OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter. + MS + MS:1001723 + This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. + ProteomeDiscoverer:4. Dynamic Modification + true + + + + + OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter. + PSI:PI + + + + + + + + + + + + + + + Static Modification for X. + MS + MS:1001724 + ProteomeDiscoverer:Static Modification for X + + + + + Static Modification for X. + PSI:MS + + + + + + + + + + + + + + + Minimal initial peptide probability to contribute to analysis. + MS + MS:1001725 + ProteomeDiscoverer:Initial minimal peptide probability + + + + + Minimal initial peptide probability to contribute to analysis. + PSI:MS + + + + + + + + + + + + + + + Minimum adjusted peptide probability contributing to protein probability. + MS + MS:1001726 + ProteomeDiscoverer:Minimal peptide probability + + + + + Minimum adjusted peptide probability contributing to protein probability. + PSI:MS + + + + + + + + + + + + + + + Minimum peptide weight contributing to protein probability. + MS + MS:1001727 + ProteomeDiscoverer:Minimal peptide weight + + + + + Minimum peptide weight contributing to protein probability. + PSI:MS + + + + + + + + + + + + + + + Number of spectra from 1+ precursor ions. + MS + MS:1001728 + ProteomeDiscoverer:Number of input1 spectra + + + + + Number of spectra from 1+ precursor ions. + PSI:MS + + + + + + + + + + + + + + + Number of spectra from 2+ precursor ions. + MS + MS:1001729 + ProteomeDiscoverer:Number of input2 spectra + + + + + Number of spectra from 2+ precursor ions. + PSI:MS + + + + + + + + + + + + + + + Number of spectra from 3+ precursor ions. + MS + MS:1001730 + ProteomeDiscoverer:Number of input3 spectra + + + + + Number of spectra from 3+ precursor ions. + PSI:MS + + + + + + + + + + + + + + + Number of spectra from 4+ precursor ions. + MS + MS:1001731 + ProteomeDiscoverer:Number of input4 spectra + + + + + Number of spectra from 4+ precursor ions. + PSI:MS + + + + + + + + + + + + + + + Number of spectra from 5+ precursor ions. + MS + MS:1001732 + ProteomeDiscoverer:Number of input5 spectra + + + + + Number of spectra from 5+ precursor ions. + PSI:MS + + + + + + + + + + + + + + + Total number of predicted correct protein ids (sum of probabilities). + MS + MS:1001733 + ProteomeDiscoverer:Number of predicted correct proteins + + + + + Total number of predicted correct protein ids (sum of probabilities). + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Sample organism (used for annotation purposes). + MS + MS:1001734 + This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. + ProteomeDiscoverer:Organism + true + + + + + OBSOLETE Sample organism (used for annotation purposes). + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Full path database name. + MS + MS:1001735 + This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. + ProteomeDiscoverer:Reference Database + true + + + + + OBSOLETE Full path database name. + PSI:MS + + + + + + + + + + + + + + + Residues considered equivalent when comparing peptides. + MS + MS:1001736 + ProteomeDiscoverer:Residue substitution list + + + + + Residues considered equivalent when comparing peptides. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE File type (if not pepXML). + MS + MS:1001737 + This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead. + ProteomeDiscoverer:Source file extension + true + + + + + OBSOLETE File type (if not pepXML). + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Input pepXML files. + MS + MS:1001738 + This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. + ProteomeDiscoverer:Source Files + true + + + + + OBSOLETE Input pepXML files. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE Input pepXML files (old). + MS + MS:1001739 + This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. + ProteomeDiscoverer:Source Files old + true + + + + + OBSOLETE Input pepXML files (old). + PSI:MS + + + + + + + + + + + + + + + Windows full path for database. + MS + MS:1001740 + ProteomeDiscoverer:WinCyg reference database + + + + + Windows full path for database. + PSI:MS + + + + + + + + + + + + + + + Windows pepXML file names. + MS + MS:1001741 + ProteomeDiscoverer:WinCyg source files + + + + + Windows pepXML file names. + PSI:MS + + + + + + + + + Finnigan LTQ Orbitrap Velos MS. + MS + MS:1001742 + LTQ Orbitrap Velos + + + + + Finnigan LTQ Orbitrap Velos MS. + PSI:MS + + + + + + + + + + + + + + + Determines if to use A ions for spectrum matching. + MS + MS:1001743 + ProteomeDiscoverer:Mascot:Weight of A Ions + + + + + Determines if to use A ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use B ions for spectrum matching. + MS + MS:1001744 + ProteomeDiscoverer:Mascot:Weight of B Ions + + + + + Determines if to use B ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use C ions for spectrum matching. + MS + MS:1001745 + ProteomeDiscoverer:Mascot:Weight of C Ions + + + + + Determines if to use C ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use D ions for spectrum matching. + MS + MS:1001746 + ProteomeDiscoverer:Mascot:Weight of D Ions + + + + + Determines if to use D ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use V ions for spectrum matching. + MS + MS:1001747 + ProteomeDiscoverer:Mascot:Weight of V Ions + + + + + Determines if to use V ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use W ions for spectrum matching. + MS + MS:1001748 + ProteomeDiscoverer:Mascot:Weight of W Ions + + + + + Determines if to use W ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use X ions for spectrum matching. + MS + MS:1001749 + ProteomeDiscoverer:Mascot:Weight of X Ions + + + + + Determines if to use X ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use Y ions for spectrum matching. + MS + MS:1001750 + ProteomeDiscoverer:Mascot:Weight of Y Ions + + + + + Determines if to use Y ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use z ions for spectrum matching. + MS + MS:1001751 + ProteomeDiscoverer:Mascot:Weight of Z Ions + + + + + Determines if to use z ions for spectrum matching. + PSI:MS + + + + + + + + + + + + + + + Determines if to use precursor reevaluation. + MS + MS:1001752 + ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation + + + + + Determines if to use precursor reevaluation. + PSI:MS + + + + + + + + + + + + + + + Signal-to-Noise ratio below which peaks are removed (in FT mode only). + MS + MS:1001753 + ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly + + + + + Signal-to-Noise ratio below which peaks are removed (in FT mode only). + PSI:MS + + + + + + + + + + + + + + + Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches. + MS + MS:1001754 + ProteomeDiscoverer:Mascot:Please Do not Touch this + + + + + Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches. + PSI:MS + + + + + + + + + + + + + + + Phone number of the contact person or organization. + MS + MS:1001755 + contact phone number + + + + + Phone number of the contact person or organization. + PSI:MS + + + + + + + + + + + + + + + Fax number for the contact person or organization. + MS + MS:1001756 + contact fax number + + + + + Fax number for the contact person or organization. + PSI:MS + + + + + + + + + + + + + + + Toll-free phone number of the contact person or organization. + MS + MS:1001757 + contact toll-free phone number + + + + + Toll-free phone number of the contact person or organization. + PSI:MS + + + + + + + + + + + + + + + Significance threshold type used in Mascot reporting (either 'identity' or 'homology'). + MS + MS:1001758 + Mascot:SigThresholdType + + + + + Significance threshold type used in Mascot reporting (either 'identity' or 'homology'). + PSI:MS + + + + + + + + + + + + + + + Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering'). + MS + MS:1001759 + Mascot:ProteinGrouping + + + + + Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering'). + PSI:MS + + + + + + + + + + + + + + + List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'. + MS + MS:1001760 + Percolator:features + + + + + List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'. + PSI:MS + + + + + + + + + Waters LC-system ACQUITY UPLC. + MS + MS:1001761 + ACQUITY UPLC + + + + + Waters LC-system ACQUITY UPLC. + PSI:MS + + + + + + + + + Waters LC-system ACQUITY UPLC H-Class. + MS + MS:1001762 + ACQUITY UPLC H-Class + + + + + Waters LC-system ACQUITY UPLC H-Class. + PSI:MS + + + + + + + + + Waters LC-system ACQUITY UPLC H-Class Bio. + MS + MS:1001763 + ACQUITY UPLC H-Class Bio + + + + + Waters LC-system ACQUITY UPLC H-Class Bio. + PSI:MS + + + + + + + + + Waters LC-system ACQUITY UPLC I-Class. + MS + MS:1001764 + ACQUITY UPLC I-Class + + + + + Waters LC-system ACQUITY UPLC I-Class. + PSI:MS + + + + + + + + + Waters LC-system ACQUITY UPLC Systems with 2D Technology. + MS + MS:1001765 + ACQUITY UPLC Systems with 2D Technology + + + + + Waters LC-system ACQUITY UPLC Systems with 2D Technology. + PSI:MS + + + + + + + + + Waters LC-system nanoACQUITY UPLC. + MS + MS:1001766 + nanoACQUITY UPLC + + + + + Waters LC-system nanoACQUITY UPLC. + PSI:MS + + + + + + + + + Waters LC-system nanoACQUITY UPLC System with 1D Technology. + MS + MS:1001767 + nanoACQUITY UPLC System with 1D Technology + + + + + Waters LC-system nanoACQUITY UPLC System with 1D Technology. + PSI:MS + + + + + + + + + Waters LC-system nanoACQUITY UPLC with HDX Technology. + MS + MS:1001768 + nanoACQUITY UPLC with HDX Technology + + + + + Waters LC-system nanoACQUITY UPLC with HDX Technology. + PSI:MS + + + + + + + + + Waters LC-system TRIZAIC UPLC nanoTile. + MS + MS:1001769 + TRIZAIC UPLC nanoTile + + + + + Waters LC-system TRIZAIC UPLC nanoTile. + PSI:MS + + + + + + + + + Waters oa-ToF based GCT Premier. + MS + MS:1001770 + GCT Premier + + + + + Waters oa-ToF based GCT Premier. + PSI:MS + + + + + + + + + Waters oa-ToF based MALDI Synapt G2 HDMS. + MS + MS:1001771 + MALDI Synapt G2 HDMS + + + + + Waters oa-ToF based MALDI Synapt G2 HDMS. + PSI:MS + + + + + + + + + Waters oa-ToF based MALDI Synapt G2 MS. + MS + MS:1001772 + MALDI Synapt G2 MS + + + + + Waters oa-ToF based MALDI Synapt G2 MS. + PSI:MS + + + + + + + + + Waters oa-ToF based MALDI Synapt G2 MS. + MS + MS:1001773 + MALDI Synapt G2-S HDMS + + + + + Waters oa-ToF based MALDI Synapt G2 MS. + PSI:MS + + + + + + + + + Waters oa-ToF based MALDI Synapt G2-S MS. + MS + MS:1001774 + MALDI Synapt G2-S MS + + + + + Waters oa-ToF based MALDI Synapt G2-S MS. + PSI:MS + + + + + + + + + Waters oa-ToF based MALDI Synapt HDMS. + MS + MS:1001775 + MALDI Synapt HDMS + + + + + Waters oa-ToF based MALDI Synapt HDMS. + PSI:MS + + + + + + + + + Waters oa-ToF based MALDI Synapt MS. + MS + MS:1001776 + MALDI Synapt MS + + + + + Waters oa-ToF based MALDI Synapt MS. + PSI:MS + + + + + + + + + Waters oa-ToF based Synapt G2 HDMS. + MS + MS:1001777 + Synapt G2 HDMS + + + + + Waters oa-ToF based Synapt G2 HDMS. + PSI:MS + + + + + + + + + Waters oa-ToF based Synapt G2 MS. + MS + MS:1001778 + Synapt G2 MS + + + + + Waters oa-ToF based Synapt G2 MS. + PSI:MS + + + + + + + + + Waters oa-ToF based Synapt G2-S HDMS. + MS + MS:1001779 + Synapt G2-S HDMS + + + + + Waters oa-ToF based Synapt G2-S HDMS. + PSI:MS + + + + + + + + + Waters oa-ToF based Synapt G2-S MS. + MS + MS:1001780 + Synapt G2-S MS + + + + + Waters oa-ToF based Synapt G2-S MS. + PSI:MS + + + + + + + + + Waters oa-ToF based Synapt HDMS. + MS + MS:1001781 + Synapt HDMS + + + + + Waters oa-ToF based Synapt HDMS. + PSI:MS + + + + + + + + + Waters oa-ToF based Synapt MS. + MS + MS:1001782 + Synapt MS + + + + + Waters oa-ToF based Synapt MS. + PSI:MS + + + + + + + + + Waters oa-ToF based Xevo G2 Q-Tof. + MS + MS:1001783 + Xevo G2 Q-Tof + + + + + Waters oa-ToF based Xevo G2 Q-Tof. + PSI:MS + + + + + + + + + Waters oa-ToF based Xevo G2 Tof. + MS + MS:1001784 + Xevo G2 Tof + + + + + Waters oa-ToF based Xevo G2 Tof. + PSI:MS + + + + + + + + + Waters oa-ToF based Xevo Q-Tof. + MS + MS:1001785 + Xevo Q-Tof + + + + + Waters oa-ToF based Xevo Q-Tof. + PSI:MS + + + + + + + + + Waters quadrupole based 3100. + MS + MS:1001786 + 3100 + + + + + Waters quadrupole based 3100. + PSI:MS + + + + + + + + + Waters quadrupole based Acquity SQD. + MS + MS:1001787 + Acquity SQD + + + + + Waters quadrupole based Acquity SQD. + PSI:MS + + + + + + + + + Waters quadrupole based Acquity TQD. + MS + MS:1001788 + Acquity TQD + + + + + Waters quadrupole based Acquity TQD. + PSI:MS + + + + + + + + + Waters (triple) quadrupole based Quattro micro GC. + MS + MS:1001789 + Quattro micro GC + + + + + Waters (triple) quadrupole based Quattro micro GC. + PSI:MS + + + + + + + + + Waters quadrupole based Xevo TQ MS. + MS + MS:1001790 + Xevo TQ MS + + + + + Waters quadrupole based Xevo TQ MS. + PSI:MS + + + + + + + + + Waters quadrupole based Xevo TQD. + MS + MS:1001791 + Xevo TQD + + + + + Waters quadrupole based Xevo TQD. + PSI:MS + + + + + + + + + Waters quadrupole based Xevo TQ-S. + MS + MS:1001792 + Xevo TQ-S + + + + + Waters quadrupole based Xevo TQ-S. + PSI:MS + + + + + + + + + + + + + + + NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences. + MS + MS:1001793 + Mascot:PreferredTaxonomy + + + + + NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences. + PSI:MS + + + + + + + + + + + Waters Empower software for liquid chromatography and mass spectrometry acquisition. + MS + MS:1001795 + Empower + + + + + Waters Empower software for liquid chromatography and mass spectrometry acquisition. + PSI:MS + + + + + + + + + + + Waters UNIFY software for liquid chromatography and mass spectrometry acquisition. + MS + MS:1001796 + UNIFY + + + + + Waters UNIFY software for liquid chromatography and mass spectrometry acquisition. + PSI:MS + + + + + + + + OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide. + TWIMS + MS + MS:1001797 + This child of the former purgatory term ion mobility spectrometry was made obsolete. + travelling wave ion mobility mass spectrometer + true + + + + + OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide. + PSI:MS + + + + + + + + + LECO software for data acquisition and analysis. + MS + MS:1001798 + LECO software + + + + + LECO software for data acquisition and analysis. + PSI:MS + + + + + + + + + + + + Software for acquisition, processing and analysis of data for LECO instruments. + MS + MS:1001799 + ChromaTOF software + + + + + Software for acquisition, processing and analysis of data for LECO instruments. + PSI:MS + + + + + + + + + LECO instrument model. + MS + MS:1001800 + LECO instrument model + + + + + LECO instrument model. + PSI:MS + + + + + + + + + LECO high resolution time-of-flight GC mass spectrometer. + MS + MS:1001801 + Pegasus HRT + + + + + LECO high resolution time-of-flight GC mass spectrometer. + PSI:MS + + + + + + + + + LECO high resolution time-of-flight LC mass spectrometer. + MS + MS:1001802 + Citius HRT + + + + + LECO high resolution time-of-flight LC mass spectrometer. + PSI:MS + + + + + + + + + LECO GC time-of-flight mass spectrometer. + MS + MS:1001803 + Pegasus + + + + + LECO GC time-of-flight mass spectrometer. + PSI:MS + + + + + + + + + LECO bench-top GC time-of-flight mass spectrometer. + MS + MS:1001804 + TruTOF + + + + + LECO bench-top GC time-of-flight mass spectrometer. + PSI:MS + + + + + + + + + The data type of the value reported in a QuantLayer. + MS + MS:1001805 + quantification datatype + + + + + The data type of the value reported in a QuantLayer. + PSI:MS + + + + + + + + + Attributes describing the details of an object relevant for reporting quantification workflows or values. + MS + MS:1001806 + quantification object attribute + + + + + Attributes describing the details of an object relevant for reporting quantification workflows or values. + PSI:MS + + + + + + + + + Attribute describing a study variable. + MS + MS:1001807 + study variable attribute + + + + + Attribute describing a study variable. + PSI:MS + + + + + + + + + + + + + + + The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'. + MS + MS:1001808 + technical replicate + + + + + The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'. + PSI:MS + + + + + + + + + The study variable is 'biological replicate'. This means, the run was generated from another individual or sample. + MS + MS:1001809 + biological replicate + + + + + The study variable is 'biological replicate'. This means, the run was generated from another individual or sample. + PSI:MS + + + + + + + + + The experimental condition is 'case' in contrast to 'control'. + MS + MS:1001810 + experimental condition 'case' + + + + + The experimental condition is 'case' in contrast to 'control'. + PSI:MS + + + + + + + + + The experimental condition is 'control' in contrast to 'case'. + MS + MS:1001811 + experimental condition 'control' + + + + + The experimental condition is 'control' in contrast to 'case'. + PSI:MS + + + + + + + + + The experimental condition is 'disease' in contrast to 'healthy'. + MS + MS:1001812 + experimental condition 'disease' + + + + + The experimental condition is 'disease' in contrast to 'healthy'. + PSI:MS + + + + + + + + + The experimental condition is 'healthy' in contrast to 'disease'. + MS + MS:1001813 + experimental condition 'healthy' + + + + + The experimental condition is 'healthy' in contrast to 'disease'. + PSI:MS + + + + + + + + + + + + + + + The experimental condition is given in the value of this term. + MS + MS:1001814 + generic experimental condition + + + + + The experimental condition is given in the value of this term. + PSI:MS + + + + + + + + + + + + + + + The experimental design followed a time series design. The time point of this run is given in the value of this term. + MS + MS:1001815 + time series, time point X + + + + + The experimental design followed a time series design. The time point of this run is given in the value of this term. + PSI:MS + + + + + + + + + + + + + + + The experimental design followed a dilution series design. The concentration of this run is given in the value of this term. + MS + MS:1001816 + dilution series, concentration X + + + + + The experimental design followed a dilution series design. The concentration of this run is given in the value of this term. + PSI:MS + + + + + + + + + Attribute describing a raw file. + MS + MS:1001817 + raw file attribute + + + + + Attribute describing a raw file. + PSI:MS + + + + + + + + + The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free). + MS + MS:1001818 + one sample run + + + + + The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free). + PSI:MS + + + + + + + + + The raw file contains the run of two samples (e.g. SILAC, metabolic labelling). + MS + MS:1001819 + two sample run + + + + + The raw file contains the run of two samples (e.g. SILAC, metabolic labelling). + PSI:MS + + + + + + + + + The raw file contains the run of three samples (e.g. 3-plex SILAC). + MS + MS:1001820 + three sample run + + + + + The raw file contains the run of three samples (e.g. 3-plex SILAC). + PSI:MS + + + + + + + + + The raw file contains the run of four samples (e.g. 4-plex iTraq). + MS + MS:1001821 + four sample run + + + + + The raw file contains the run of four samples (e.g. 4-plex iTraq). + PSI:MS + + + + + + + + + The raw file contains the run of eight samples (e.g. 8-plex iTraq). + MS + MS:1001822 + eight sample run + + + + + The raw file contains the run of eight samples (e.g. 8-plex iTraq). + PSI:MS + + + + + + + + + Attribute describing, how raw files build a raw file group. + MS + MS:1001823 + raw files group attribute + + + + + Attribute describing, how raw files build a raw file group. + PSI:MS + + + + + + + + + Attribute describing, how raw files build a raw file group. + MS + MS:1001824 + merge of runs of 1D gel bands + + + + + Attribute describing, how raw files build a raw file group. + PSI:MS + + + + + + + + + Attribute describing a feature list. + MS + MS:1001825 + feature list attribute + + + + + Attribute describing a feature list. + PSI:MS + + + + + + + + + The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given. + MS + MS:1001826 + mass trace reporting: rectangles + + + + + The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given. + PSI:MS + + + + + + + + + The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit. + MS + MS:1001827 + mass trace reporting: polygons + + + + + The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit. + PSI:MS + + + + + + + + + Attribute describing a feature. + MS + MS:1001828 + feature attribute + + + + + Attribute describing a feature. + PSI:MS + + + + + + + + + + + + + + + Identifier for an SRM transition in an external document describing additional information about the transition. + MS + MS:1001829 + SRM transition ID + + + + + Identifier for an SRM transition in an external document describing additional information about the transition. + PSI:MS + + + + + + + + + Software from Nonlinear Dynamics for LC-MS label-free workflow. + MS + MS:1001830 + Progenesis LC-MS + + + + + Software from Nonlinear Dynamics for LC-MS label-free workflow. + PSI:MS + + + + + + + + + + Software for SILAC workflow. + MS + MS:1001831 + SILACAnalyzer + + + + + Software for SILAC workflow. + PSI:MS + + + + + + + + + + + + + + + Quantitation software comment or any customizations to the default setup of the software. + MS + MS:1001832 + quantitation software comment or customizations + + + + + Quantitation software comment or any customizations to the default setup of the software. + PSI:PI + + + + + + + + + The overall workflow of this quantitation report. + MS + MS:1001833 + quantitation analysis summary + + + + + The overall workflow of this quantitation report. + PSI:PI + + + + + + + + + LC-MS label-free workflow (RT m/z map). + MS + MS:1001834 + LC-MS label-free quantitation analysis + + + + + LC-MS label-free workflow (RT m/z map). + PSI:PI + + + + + + + + + SILAC workflow (heavy, light, and sometimes medium peak). + MS + MS:1001835 + SILAC quantitation analysis + + + + + SILAC workflow (heavy, light, and sometimes medium peak). + PSI:PI + + + + + + + + + Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant). + MS + MS:1001836 + spectral counting quantitation analysis + + + + + Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant). + PSI:PI + + + + + + + + + Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range. + MS + MS:1001837 + iTRAQ quantitation analysis + + + + + Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range. + PMID:15385600 + PSI:PI + + + + + + + + + Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). + MS + MS:1001838 + SRM quantitation analysis + + + + + Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). + PSI:PI + + + + + + + + + Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens). + MS + MS:1001839 + metabolic labeling 14N / 15N quantitation analysis + + + + + Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens). + PSI:PI + + + + + + + + + + + + + + + Maximum peak intensity of the LC-MS feature. + MS + MS:1001840 + LC-MS feature intensity + + + + + Maximum peak intensity of the LC-MS feature. + PSI:PI + + + + + + + + + + + + + + + Real (intensity times area) volume of the LC-MS feature. + MS + MS:1001841 + LC-MS feature volume + + + + + Real (intensity times area) volume of the LC-MS feature. + PSI:PI + + + + + + + + + + + + + + + The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting. + MS + MS:1001842 + sequence-level spectral count + + + + + The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting. + PSI:PI + + + + + + + + + + + + + + + Maximum intensity of MS1 feature. + MS + MS:1001843 + MS1 feature maximum intensity + + + + + Maximum intensity of MS1 feature. + PSI:PI + + + + + + + + + + + + + + + Area of MS1 feature. + MS + MS:1001844 + MS1 feature area + + + + + Area of MS1 feature. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE Area of MS1 peak (e.g. SILAC, 15N). + MS + MS:1001845 + This term was made obsolete because it was a duplication of MS:1001844. + peak area + true + + + + + OBSOLETE Area of MS1 peak (e.g. SILAC, 15N). + PSI:PI + + + + + + + + + + + + + + + Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N). + MS + MS:1001846 + isotopic pattern area + + + + + Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N). + PSI:PI + + + + + + + + + + + + + + + Intensity of MS2 reporter ion (e.g. iTraq). + MS + MS:1001847 + reporter ion intensity + + + + + Intensity of MS2 reporter ion (e.g. iTraq). + PSI:PI + + + + + + + + + Simple ratio of two values (enumerator and denominator). + MS + MS:1001848 + simple ratio of two values + + + + + Simple ratio of two values (enumerator and denominator). + PSI:PI + + + + + + + + + + + + + + + OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values. + MS + MS:1001849 + This term was made obsolete because the concept MatchedFeature was dropped. + sum of MatchedFeature values + true + + + + + OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values. + PSI:PI + + + + + + + + + + + + + + + Normalized peptide value. + MS + MS:1001850 + normalized peptide value + + + + + Normalized peptide value. + PSI:PI + + + + + + + + + + + + + + + Protein quantification value calculated as sum of peptide values. + MS + MS:1001851 + protein value: sum of peptide values + + + + + Protein quantification value calculated as sum of peptide values. + PSI:PI + + + + + + + + + + + + + + + Normalized protein value. + MS + MS:1001852 + normalized protein value + + + + + Normalized protein value. + PSI:PI + + + + + + + + + + + + + + + Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis). + MS + MS:1001853 + max fold change + + + + + Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis). + PSI:PI + + + + + + + + + + + + + + + Global datatype: p-value of ANOVA of group means (e.g. Progenesis). + MS + MS:1001854 + ANOVA p-value + + + + + Global datatype: p-value of ANOVA of group means (e.g. Progenesis). + PSI:PI + + + + + + + + + + + + + + + P-value of t-Test of two groups. + MS + MS:1001855 + t-test p-value + + + + + P-value of t-Test of two groups. + PSI:PI + + + + + + + + + + + + + + + Intensity (or area) of MS2 reporter ion (e.g. iTraq). + MS + MS:1001856 + reporter ion raw value + + + + + Intensity (or area) of MS2 reporter ion (e.g. iTraq). + PSI:PI + + + + + + + + + + + + + + + Normalized value of MS2 reporter ion (e.g. iTraq). + MS + MS:1001857 + reporter ion normalized value + + + + + Normalized value of MS2 reporter ion (e.g. iTraq). + PSI:PI + + + + + + + + + + + + + + + Area of the extracted ion chromatogram (e.g. of a transition in SRM). + MS + MS:1001858 + XIC area + + + + + Area of the extracted ion chromatogram (e.g. of a transition in SRM). + PSI:PI + + + + + + + + + + + + + + + Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM). + MS + MS:1001859 + normalized XIC area + + + + + Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM). + PSI:PI + + + + + + + + + + + + + + + Protein quantification value calculated as mean of peptide ratios. + MS + MS:1001860 + protein value: mean of peptide ratios + + + + + Protein quantification value calculated as mean of peptide ratios. + PSI:PI + + + + + + + + + + + + + + Terms used to describe types of quantification data processing. + MS + MS:1001861 + quantification data processing + + + + + Terms used to describe types of quantification data processing. + PSI:MS + + + + + + + + + Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting). + MS + MS:1001862 + normalization to mean of sum of all proteins + + + + + Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting). + PSI:MS + + + + + + + + + Normalization of protein values to approach the same distribution. + MS + MS:1001863 + quantile normalization, proteins + + + + + Normalization of protein values to approach the same distribution. + PSI:MS + + + + + + + + + Normalization of peptide values to approach the same distribution. + MS + MS:1001864 + quantile normalization, peptides + + + + + Normalization of peptide values to approach the same distribution. + PSI:MS + + + + + + + + + Automatic RT alignment of Progenesis software. + MS + MS:1001865 + Progenesis automatic alignment + + + + + Automatic RT alignment of Progenesis software. + PSI:MS + + + + + + + + + RT alignment of Progenesis software using automatic and manual vectors. + MS + MS:1001866 + Progenesis manual alignment + + + + + RT alignment of Progenesis software using automatic and manual vectors. + PSI:MS + + + + + + + + + Normalization as performed by Progenesis LC-MS. + MS + MS:1001867 + Progenesis normalization + + + + + Normalization as performed by Progenesis LC-MS. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry). + MS + MS:1001868 + distinct peptide-level q-value + + + + + Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry). + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the q-value for proteins. + MS + MS:1001869 + protein-level q-value + + + + + Estimation of the q-value for proteins. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + MS + MS:1001870 + peptide sequence-level p-value + + + + + Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the p-value for proteins. + MS + MS:1001871 + protein-level p-value + + + + + Estimation of the p-value for proteins. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + MS + MS:1001872 + peptide sequence-level e-value + + + + + Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the e-value for proteins. + MS + MS:1001873 + protein-level e-value + + + + + Estimation of the e-value for proteins. + PSI:PI + + + + + + + + + + + + + + + + OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0. + MS + MS:1001874 + This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374). + FDRScore + true + + + + + OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0. + PMID:19253293 + + + + + + + + + + + + + + + The regular expression describing the sequence motif for a modification. + MS + MS:1001875 + modification motif + + + + + The regular expression describing the sequence motif for a modification. + PSI:PI + + + + + + + + + The a priori probability of a modification. + MS + MS:1001876 + modification probability + + + + + The a priori probability of a modification. + PSI:PI + + + + + + + + + + + + Software for acquisition, processing and analysis of data for LECO instruments. + MS + MS:1001877 + ChromaTOF HRT software + + + + + Software for acquisition, processing and analysis of data for LECO instruments. + PSI:MS + + + + + + + + + Shimadzu Biotech software for data acquisition, processing, and analysis. + MS + MS:1001878 + MALDI Solutions Microbial Identification + + + + + Shimadzu Biotech software for data acquisition, processing, and analysis. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation. + MS + MS:1001879 + offset voltage + + + + + The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation. + PSI:MS + + + + + + + + + The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum. + MS + MS:1001880 + in-source collision-induced dissociation + + + + + The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum. + PSI:MS + + + + + + + + + mz5 file format, modelled after mzML. + MS + MS:1001881 + mz5 format + + + + + mz5 file format, modelled after mzML. + PSI:MS + + + + + + + + + + + + + + Attributes of the quality of a transition that affect its selection as appropriate. + MS + MS:1001882 + transition validation attribute + + + + + Attributes of the quality of a transition that affect its selection as appropriate. + PSI:MS + + + + + + + + + + + + + + + Variation of a set of signal measurements calculated as the standard deviation relative to the mean. + MS + MS:1001883 + coefficient of variation + + + + + Variation of a set of signal measurements calculated as the standard deviation relative to the mean. + PSI:MS + + + + + + + + + + + + + + + Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal. + MS + MS:1001884 + signal-to-noise ratio + + + + + Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal. + PSI:MS + + + + + + + + + + + + + + + + Parameters string passed to a command-line interface software application, omitting the executable name. + MS + MS:1001885 + command-line parameters + + + + + Parameters string passed to a command-line interface software application, omitting the executable name. + PSI:MS + + + + + + + + + + Software for data analysis of peptides and proteins. + MS + MS:1001886 + SQID + + + + + Software for data analysis of peptides and proteins. + PSI:MS + + + + + + + + + The SQID result 'Score'. + MS + MS:1001887 + SQID:score + + + + + The SQID result 'Score'. + PSI:PI + + + + + + + + + The SQID result 'deltaScore'. + MS + MS:1001888 + SQID:deltaScore + + + + + The SQID result 'deltaScore'. + PSI:PI + + + + + + + + + The SQID result 'protein score'. + MS + MS:1001889 + SQID:protein score + + + + + The SQID result 'protein score'. + PSI:PI + + + + + + + + + + + + + + + The data type normalised abundance for proteins produced by Progenesis LC-MS. + MS + MS:1001890 + Progenesis:protein normalised abundance + + + + + The data type normalised abundance for proteins produced by Progenesis LC-MS. + PSI:MS + + + + + + + + + + + + + + + The data type normalised abundance for peptides produced by Progenesis LC-MS. + MS + MS:1001891 + Progenesis:peptide normalised abundance + + + + + The data type normalised abundance for peptides produced by Progenesis LC-MS. + PSI:MS + + + + + + + + + + + + + + + The data type raw abundance for proteins produced by Progenesis LC-MS. + MS + MS:1001892 + Progenesis:protein raw abundance + + + + + The data type raw abundance for proteins produced by Progenesis LC-MS. + PSI:MS + + + + + + + + + + + + + + + The data type raw abundance for peptide produced by Progenesis LC-MS. + MS + MS:1001893 + Progenesis:peptide raw abundance + + + + + The data type raw abundance for peptide produced by Progenesis LC-MS. + PSI:MS + + + + + + + + + + + + + + + The data type confidence score produced by Progenesis LC-MS. + MS + MS:1001894 + Progenesis:confidence score + + + + + The data type confidence score produced by Progenesis LC-MS. + PSI:MS + + + + + + + + + + + + + + + The data type peptide count produced by Progenesis LC-MS. + MS + MS:1001895 + Progenesis:peptide count + + + + + The data type peptide count produced by Progenesis LC-MS. + PSI:MS + + + + + + + + + + + + + + + The data type feature intensity produced by Progenesis LC-MS. + MS + MS:1001896 + Progenesis:feature intensity + + + + + The data type feature intensity produced by Progenesis LC-MS. + PSI:MS + + + + + + + + + + + + + + + The data type peptide counts (unique) produced by MaxQuant. + MS + MS:1001897 + MaxQuant:peptide counts (unique) + + + + + The data type peptide counts (unique) produced by MaxQuant. + PSI:MS + + + + + + + + + + + + + + + The data type peptide counts (all) produced by MaxQuant. + MS + MS:1001898 + MaxQuant:peptide counts (all) + + + + + The data type peptide counts (all) produced by MaxQuant. + PSI:MS + + + + + + + + + + + + + + + The data type peptide counts (razor+unique) produced by MaxQuant. + MS + MS:1001899 + MaxQuant:peptide counts (razor+unique) + + + + + The data type peptide counts (razor+unique) produced by MaxQuant. + PSI:MS + + + + + + + + + + + + + + + The data type sequence length produced by MaxQuant. + MS + MS:1001900 + MaxQuant:sequence length + + + + + The data type sequence length produced by MaxQuant. + PSI:MS + + + + + + + + + + + + + + + The data type PEP (posterior error probability) produced by MaxQuant. + MS + MS:1001901 + MaxQuant:PEP + + + + + The data type PEP (posterior error probability) produced by MaxQuant. + PSI:MS + + + + + + + + + + + + + + + The data type LFQ intensity produced by MaxQuant. + MS + MS:1001902 + MaxQuant:LFQ intensity + + + + + The data type LFQ intensity produced by MaxQuant. + PSI:MS + + + + + + + + + + + + + + + The data type feature intensity produced by MaxQuant. + MS + MS:1001903 + MaxQuant:feature intensity + + + + + The data type feature intensity produced by MaxQuant. + PSI:MS + + + + + + + + + + + + + + + The data type MS2 count produced by MaxQuant. + MS + MS:1001904 + MaxQuant:MS/MS count + + + + + The data type MS2 count produced by MaxQuant. + PSI:MS + + + + + + + + + + + + + + + The emPAI value of protein abundance, produced from the emPAI algorithm. + MS + MS:1001905 + emPAI value + + + + + The emPAI value of protein abundance, produced from the emPAI algorithm. + PSI:MS + + + + + + + + + + + + + + + The APEX value of protein abundance, produced from the APEX software. + MS + MS:1001906 + APEX value + + + + + The APEX value of protein abundance, produced from the APEX software. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The full width of a retention time window for a chromatographic peak. + MS + MS:1001907 + retention time window width + + + + + The full width of a retention time window for a chromatographic peak. + PSI:MS + + + + + + + + + Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source. + MS + MS:1001908 + ISQ + + + + + Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source. + PSI:MS + + + + + + + + + Thermo Scientific second generation Velos. + MS + MS:1001909 + Velos Plus + + + + + Thermo Scientific second generation Velos. + PSI:MS + + + + + + + + + Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite. + MS + MS:1001910 + LTQ Orbitrap Elite + + + + + Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite. + PSI:MS + + + + + + + + + Thermo Scientific Q Exactive. + MS + MS:1001911 + Q Exactive + + + + + Thermo Scientific Q Exactive. + PSI:MS + + + + + + + + + + + Thermo Scientific PinPoint SRM analysis software. + MS + MS:1001912 + PinPoint + + + + + Thermo Scientific PinPoint SRM analysis software. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts. + MS + MS:1001913 + S-lens voltage + + + + + Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts. + PSI:MS + + + + + + + + + Python module to interface mzML Data. + MS + MS:1001914 + pymzML + + + + + Python module to interface mzML Data. + PSI:MS + + + + + + + + + + + + + + + Enzyme leukocyte elastase (EC 3.4.21.37). + MS + MS:1001915 + leukocyte elastase + + + + + Enzyme leukocyte elastase (EC 3.4.21.37). + BRENDA:3.4.21.37 + + + + + + + + + + + + + + + Enzyme proline endopeptidase (EC 3.4.21.26). + MS + MS:1001916 + proline endopeptidase + + + + + Enzyme proline endopeptidase (EC 3.4.21.26). + BRENDA:3.4.21.26 + + + + + + + + + + + + + + + Enzyme glutamyl endopeptidase (EC 3.4.21.19). + Glu-C + staphylococcal protease + MS + MS:1001917 + glutamyl endopeptidase + + + + + Enzyme glutamyl endopeptidase (EC 3.4.21.19). + BRENDA:3.4.21.19 + + + + + + + + + + + + + + + Chemical iodobenzoate. Cleaves after W. + MS + MS:1001918 + 2-iodobenzoate + + + + + Chemical iodobenzoate. Cleaves after W. + PubChem_Compound:4739928 + + + + + + + + + + + + + + + Main identifier of a ProteomeXchange dataset. + MS + MS:1001919 + ProteomeXchange accession number + + + + + Main identifier of a ProteomeXchange dataset. + PSI:PI + + + + + + + + + + + + + + + Version number of a ProteomeXchange accession number. + MS + MS:1001921 + ProteomeXchange accession number version number + + + + + Version number of a ProteomeXchange accession number. + PSI:PI + + + + + + + + + + + + + + + + + + + + + DOI unique identifier of a publication. + doi + MS + MS:1001922 + Digital Object Identifier (DOI) + + + + + DOI unique identifier of a publication. + PSI:PI + http://dx.doi.org + + + + + + + + + + + + + + + Free text attribute that can enrich the information about an entity. + MS + MS:1001923 + external reference keyword + + + + + Free text attribute that can enrich the information about an entity. + PSI:PI + + + + + + + + + + + + + + + Keyword present in a scientific publication. + MS + MS:1001924 + journal article keyword + + + + + Keyword present in a scientific publication. + PSI:PI + + + + + + + + + + + + + + + Keyword assigned by the data submitter. + MS + MS:1001925 + submitter keyword + + + + + Keyword assigned by the data submitter. + PSI:PI + + + + + + + + + + + + + + + Keyword assigned by a data curator. + MS + MS:1001926 + curator keyword + + + + + Keyword assigned by a data curator. + PSI:PI + + + + + + + + + + + + + + + Hash assigned by the Tranche resource to an individual file. + MS + MS:1001927 + Tranche file hash + + + + + Hash assigned by the Tranche resource to an individual file. + PSI:PI + + + + + + + + + + + + + + + Hash assigned by the Tranche resource to a whole project. + MS + MS:1001928 + Tranche project hash + + + + + Hash assigned by the Tranche resource to a whole project. + PSI:PI + + + + + + + + + + + + + + + URI that allows the access to one experiment in the PRIDE database. + MS + MS:1001929 + PRIDE experiment URI + + + + + URI that allows the access to one experiment in the PRIDE database. + PSI:PI + + + + + + + + + + + + + + + URI that allows the access to one project in the PRIDE database. + MS + MS:1001930 + PRIDE project URI + + + + + URI that allows the access to one project in the PRIDE database. + PSI:PI + + + + + + + + + + + + + + The source interface. + MS + MS:1001931 + source interface + + + + + The source interface. + PSI:MS + + + + + + + + + + + + + + + + + + + + The source interface model. + MS + MS:1001932 + source interface model + + + + + The source interface model. + PSI:MS + + + + + + + + + + + + + + + + + + + + The source sprayer. + MS + MS:1001933 + source sprayer + + + + + The source sprayer. + PSI:MS + + + + + + + + + + + + + + The source sprayer type. + MS + MS:1001934 + source sprayer type + + + + + The source sprayer type. + PSI:MS + + + + + + + + + + + + + + + + + + + + The source sprayer manufacturer. + MS + MS:1001935 + source sprayer manufacturer + + + + + The source sprayer manufacturer. + PSI:MS + + + + + + + + + + + + + + + + + + + + The source sprayer model. + MS + MS:1001936 + source sprayer model + + + + + The source sprayer model. + PSI:MS + + + + + + + + + + + + + + Plate where the sample solution is spotted in a MALDI or similar instrument. + MS + MS:1001937 + sample plate + + + + + Plate where the sample solution is spotted in a MALDI or similar instrument. + PSI:MS + + + + + + + + + + + + + + The sample plate type. + MS + MS:1001938 + sample plate type + + + + + The sample plate type. + PSI:MS + + + + + + + + + Stainless steel plate. + MS + MS:1001939 + stainless steel plate + + + + + Stainless steel plate. + PSI:MS + + + + + + + + + Coated glass plate. + MS + MS:1001940 + coated glass plate + + + + + Coated glass plate. + PSI:MS + + + + + + + + + + + + + + Whether the sprayer is fed or is loaded with sample once. + MS + MS:1001941 + electrospray supply type + + + + + Whether the sprayer is fed or is loaded with sample once. + PSI:MS + + + + + + + + + The sprayer is loaded with sample once. + MS + MS:1001942 + static supply electrospray + + + + + The sprayer is loaded with sample once. + PSI:MS + + + + + + + + + The sprayer is continuously fed with sample. + MS + MS:1001943 + fed supply electrospray + + + + + The sprayer is continuously fed with sample. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts. + CXP + MS + MS:1001944 + Collision cell exit potential + + + + + Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts. + PSI:MS + + + + + + + + + LECO nominal mass resolution time-of-flight GCxGC mass spectrometer. + MS + MS:1001945 + Pegasus 4D + + + + + LECO nominal mass resolution time-of-flight GCxGC mass spectrometer. + PSI:MS + + + + + + + + + + + PEAKS Studio software for data analysis. + MS + MS:1001946 + PEAKS Studio + + + + + PEAKS Studio software for data analysis. + PSI:MS + + + + + + + + + + + PEAKS Online software for high throughput data analysis. + MS + MS:1001947 + PEAKS Online + + + + + PEAKS Online software for high throughput data analysis. + PSI:MS + + + + + + + + + + + PEAKS Node software for high throughput data analysis. + MS + MS:1001948 + PEAKS Node + + + + + PEAKS Node software for high throughput data analysis. + PSI:MS + + + + + + + + + Bioinformatics Solutions Inc. Software for data processing and analysis. + MS + MS:1001949 + BSI software + + + + + Bioinformatics Solutions Inc. Software for data processing and analysis. + PSI:MS + + + + + + + + + + + + + + + The PEAKS peptide '-10lgP Score'. + MS + MS:1001950 + PEAKS:peptideScore + + + + + The PEAKS peptide '-10lgP Score'. + PSI:MS + + + + + + + + + + + + + + + The PEAKS protein '-10lgP Score'. + MS + MS:1001951 + PEAKS:proteinScore + + + + + The PEAKS protein '-10lgP Score'. + PSI:MS + + + + + + + + + + + + + + + The ZCore probability score. + MS + MS:1001952 + ZCore:probScore + + + + + The ZCore probability score. + PSI:MS + + + + + + + + + + + + + + + + + + + + The source interface manufacturer. + MS + MS:1001953 + source interface manufacturer + + + + + The source interface manufacturer. + PSI:MS + + + + + + + + + + + + + + + + + + + + Parameters used in the mass spectrometry acquisition. + MS + MS:1001954 + acquisition parameter + + + + + Parameters used in the mass spectrometry acquisition. + PSI:MS + + + + + + + + + No cleavage. + MS + MS:1001955 + no cleavage + + + + + No cleavage. + PSI:MS + + + + + + + + + Unspecific cleavage. + MS + MS:1001956 + unspecific cleavage + + + + + Unspecific cleavage. + PSI:MS + + + + + + + + + Regular expression for leukocyte elastase. + MS + MS:1001957 + (?<=[ALIV])(? + + + + + Regular expression for leukocyte elastase. + PSI:PI + + + + + + + + + Regular expression for proline endopeptidase. + MS + MS:1001958 + (?<=[HKR]P)(? + + + + + Regular expression for proline endopeptidase. + PSI:PI + + + + + + + + + Regular expression for glutamyl endopeptidase. + MS + MS:1001959 + (?<=[^E]E) + + + + + Regular expression for glutamyl endopeptidase. + PSI:PI + + + + + + + + + Regular expression for 2-iodobenzoate. + MS + MS:1001960 + (?<=W) + + + + + Regular expression for 2-iodobenzoate. + PSI:PI + + + + + + + + + + + + + + + + + + + + Algorithm used to score the match between a spectrum and a peptide ion. + MS + MS:1001961 + peptide spectrum match scoring algorithm + + + + + Algorithm used to score the match between a spectrum and a peptide ion. + PSI:MS + + + + + + + + + + + + + + + C13 peaks to use in peak detection. + MS + MS:1001962 + Mascot:C13 counts + + + + + C13 peaks to use in peak detection. + PSI:MS + + + + + + + + + + + + + + + Weighting factor for protein list compilation by ProteinExtractor. + MS + MS:1001963 + ProteinExtractor:Weighting + + + + + Weighting factor for protein list compilation by ProteinExtractor. + PSI:MS + + + + + + + + + + + + + + + Flag indicating a second round search with Mascot. + MS + MS:1001964 + ProteinScape:second round Mascot + + + + + Flag indicating a second round search with Mascot. + PSI:MS + + + + + + + + + + + + + + + Flag indicating a second round search with Phenyx. + MS + MS:1001965 + ProteinScape:second round Phenyx + + + + + Flag indicating a second round search with Phenyx. + PSI:MS + + + + + + + + + The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry. + MS + MS:1001966 + product ion mobility + + + + + The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry. + PSI:MS + + + + + + + + + + + + + + + + + + + + + OBSOLETE The ion drift time of an MS2 product ion. + MS + MS:1001967 + This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476). + product ion drift time + true + + + + + OBSOLETE The ion drift time of an MS2 product ion. + PSI:MS + + + + + + + + + Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level. + MS + MS:1001968 + PTM localization PSM-level statistic + + + + + Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level. + PSI:MS + + + + + + + + + + + + + + + + + + + + + phosphoRS score for PTM site location at the PSM-level. + MS + MS:1001969 + phosphoRS score + + + + + phosphoRS score for PTM site location at the PSM-level. + DOI:10.1021/pr200611n + PMID:22073976 + + + + + + + + + + + + + + + + + + + + + Probability that the respective isoform is correct. + MS + MS:1001970 + phosphoRS sequence probability + + + + + Probability that the respective isoform is correct. + DOI:10.1021/pr200611n + PMID:22073976 + + + + + + + + + + + + + + + + + + + + + Estimate of the probability that the respective site is truly phosphorylated. + MS + MS:1001971 + phosphoRS site probability + + + + + Estimate of the probability that the respective site is truly phosphorylated. + DOI:10.1021/pr200611n + PMID:22073976 + + + + + + + + + + + + + + + Version of the post-translational modification scoring algorithm. + MS + MS:1001972 + PTM scoring algorithm version + + + + + Version of the post-translational modification scoring algorithm. + PSI:MS + + + + + + + + + DeBunker software. + MS + MS:1001973 + DeBunker + + + + + DeBunker software. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + Score specific to DeBunker. + MS + MS:1001974 + DeBunker:score + + + + + Score specific to DeBunker. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value. + m/z difference + MS + MS:1001975 + delta m/z + + + + + The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value. + mass difference + MS + MS:1001976 + delta M + + + + + The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value. + PSI:MS + + + + + + + + + MSQuant software. + MS + MS:1001977 + MSQuant + + + + + MSQuant software. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The PTM score from MSQuant software. + MS + MS:1001978 + MSQuant:PTM-score + + + + + The PTM score from MSQuant software. + DOI:10.1021/pr900721e + PMID:19888749 + + + + + + + + + + + + + + + + + + + + + The PTM score from MaxQuant software. + MS + MS:1001979 + MaxQuant:PTM Score + + + + + The PTM score from MaxQuant software. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The Phospho (STY) Probabilities from MaxQuant software. + MS + MS:1001980 + MaxQuant:Phospho (STY) Probabilities + + + + + The Phospho (STY) Probabilities from MaxQuant software. + PSI:MS + + + + + + + + + + + + + + + The Phospho (STY) Score Diffs from MaxQuant software. + MS + MS:1001981 + MaxQuant:Phospho (STY) Score Diffs + + + + + The Phospho (STY) Score Diffs from MaxQuant software. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The P-site localization probability value from MaxQuant software. + MS + MS:1001982 + MaxQuant:P-site localization probability + + + + + The P-site localization probability value from MaxQuant software. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest). + MS + MS:1001983 + MaxQuant:PTM Delta Score + + + + + The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest). + PSI:MS + + + + + + + + + Ascore software. + MS + MS:1001984 + Ascore software + + + + + Ascore software. + PSI:MS + + + + + + + + + + + + + + + + + + + + + A-score for PTM site location at the PSM-level. + MS + MS:1001985 + Ascore + + + + + A-score for PTM site location at the PSM-level. + DOI:10.1038/nbt1240 + PMID:16964243 + + + + + + + + + + + + + + + + + + + + + H-Score for peptide phosphorylation site location. + MS + MS:1001986 + H-Score + + + + + H-Score for peptide phosphorylation site location. + DOI:10.1021/pr1006813 + PMID:20836569 + + + + + + + + + Vacuum-drying MALDI sample preparation crystallization method. + MS + MS:1001987 + vacuum drying MALDI sample preparation + + + + + Vacuum-drying MALDI sample preparation crystallization method. + PSI:MS + + + + + + + + + Crushed-crystal MALDI sample preparation method. + MS + MS:1001988 + crushed crystal MALDI sample preparation + + + + + Crushed-crystal MALDI sample preparation method. + PSI:MS + + + + + + + + + Fast-evaporation MALDI sample preparation method. + MS + MS:1001989 + fast evaporation MALDI sample preparation + + + + + Fast-evaporation MALDI sample preparation method. + DOI:10.1021/ac00091a044 + + + + + + + + + Overlayer method combining features of the crushed-crystal method and the fast-evaporation method. + MS + MS:1001990 + overlayer MALDI sample preparation + + + + + Overlayer method combining features of the crushed-crystal method and the fast-evaporation method. + PSI:MS + + + + + + + + + Sandwich MALDI sample preparation method. + MS + MS:1001991 + sandwich MALDI sample preparation + + + + + Sandwich MALDI sample preparation method. + DOI:10.1002/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.3.CO;2-4 + + + + + + + + + Spin coating MALDI sample preparation method. + MS + MS:1001992 + spin coating MALDI sample preparation + + + + + Spin coating MALDI sample preparation method. + DOI:10.1021/cc0500710 + PMID:16283807 + + + + + + + + + Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling. + MS + MS:1001993 + quick and dirty MALDI sample preparation + + + + + Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling. + PSI:MS + + + + + + + + + Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'. + MS + MS:1001994 + top hat baseline reduction + + + + + Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'. + PSI:MS + + + + + + + + + Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures. + MS + MS:1001995 + convex hull baseline reduction + + + + + Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures. + PSI:MS + + + + + + + + + The spectrum that will be baseline subtracted is divided into a number of segments. + MS + MS:1001996 + median baseline reduction + + + + + The spectrum that will be baseline subtracted is divided into a number of segments. + PSI:MS + + + + + + + + + The random noise is removed by using the undecimated wavelet transform. + MS + MS:1001997 + wavelet transformation smoothing + + + + + The random noise is removed by using the undecimated wavelet transform. + DOI:10.1093/bioinformatics/btl355 + PMID:16820428 + + + + + + + + + It searches for known patterns in the measured spectrum. + SNAP + MS + MS:1001998 + sophisticated numerical annotation procedure + + + + + It searches for known patterns in the measured spectrum. + DOI:10.1021/ac951158i + PMID:21619291 + + + + + + + + + Normalization of areas below the curves. + MS + MS:1001999 + area normalization + + + + + Normalization of areas below the curves. + PSI:MS + + + + + + + + + A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID. + MS + MS:1002000 + LIFT + + + + + A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID. + DOI:10.1007/s00216-003-2057-0 + PMID:12830354 + + + + + + + + + + + + + + + MS1 label-based raw feature quantitation. + MS + MS:1002001 + MS1 label-based raw feature quantitation + + + + + MS1 label-based raw feature quantitation. + PSI:PI + + + + + + + + + + + + + + + MS1 label-based peptide level quantitation. + MS + MS:1002002 + MS1 label-based peptide level quantitation + + + + + MS1 label-based peptide level quantitation. + PSI:PI + + + + + + + + + + + + + + + MS1 label-based protein level quantitation. + MS + MS:1002003 + MS1 label-based protein level quantitation + + + + + MS1 label-based protein level quantitation. + PSI:PI + + + + + + + + + + + + + + + MS1 label-based proteingroup level quantitation. + MS + MS:1002004 + MS1 label-based proteingroup level quantitation + + + + + MS1 label-based proteingroup level quantitation. + PSI:PI + + + + + + + + + A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys. + MS + MS:1002005 + iRT retention time normalization standard + + + + + A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys. + DOI:10.1002/pmic.201100463 + http://www.biognosys.ch/products/rt-kit.html + + + + + + + + + + + + + + The type of the transitions, e.g. target or decoy. + MRM transition type + MS + MS:1002006 + SRM transition type + + + + + The type of the transitions, e.g. target or decoy. + PSI:MS + + + + + + + + + A transition used to target a specific compound that may be in the sample. + target MRM transition + MS + MS:1002007 + target SRM transition + + + + + A transition used to target a specific compound that may be in the sample. + PSI:MS + + + + + + + + + A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows. + decoy MRM transition + MS + MS:1002008 + decoy SRM transition + + + + + A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows. + PSI:MS + + + + + + + + + Quantitation analysis using an isobaric labelling workflow. + MS + MS:1002009 + isobaric label quantitation analysis + + + + + Quantitation analysis using an isobaric labelling workflow. + PSI:PI + + + + + + + + + Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z. + MS + MS:1002010 + TMT quantitation analysis + + + + + Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z. + PMID:12713048 + PSI:PI + + + + + + + + + Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure. + DESI + MS + MS:1002011 + desorption electrospray ionization + + + + + Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure. + DOI:10.1126/science.1104404 + PMID:15486296 + + + + + + + + + + + + + + + + + + + + + Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score). + MS + MS:1002012 + Mascot:PTM site assignment confidence + + + + + Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score). + http://www.matrixscience.com/help/pt_mods_help.html#SITE + + + + + + + + + + + + + + + + + + + + + Collision energy at the start of the collision energy ramp. + MS + MS:1002013 + collision energy ramp start + + + + + Collision energy at the start of the collision energy ramp. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Collision energy at the end of the collision energy ramp. + MS + MS:1002014 + collision energy ramp end + + + + + Collision energy at the end of the collision energy ramp. + PSI:PI + + + + + + + + + + + + + + + Spectral count peptide level quantitation. + MS + MS:1002015 + spectral count peptide level quantitation + + + + + Spectral count peptide level quantitation. + PSI:PI + + + + + + + + + + + + + + + Spectral count protein level quantitation. + MS + MS:1002016 + spectral count protein level quantitation + + + + + Spectral count protein level quantitation. + PSI:PI + + + + + + + + + + + + + + + Spectral count proteingroup level quantitation. + MS + MS:1002017 + spectral count proteingroup level quantitation + + + + + Spectral count proteingroup level quantitation. + PSI:PI + + + + + + + + + MS1 label-based analysis. + MS + MS:1002018 + MS1 label-based analysis + + + + + MS1 label-based analysis. + PSI:PI + + + + + + + + + + + + + + + Label-free raw feature quantitation. + MS + MS:1002019 + label-free raw feature quantitation + + + + + Label-free raw feature quantitation. + PSI:PI + + + + + + + + + + + + + + + Label-free peptide level quantitation. + MS + MS:1002020 + label-free peptide level quantitation + + + + + Label-free peptide level quantitation. + PSI:PI + + + + + + + + + + + + + + + Label-free protein level quantitation. + MS + MS:1002021 + label-free protein level quantitation + + + + + Label-free protein level quantitation. + PSI:PI + + + + + + + + + + + + + + + Label-free proteingroup level quantitation. + MS + MS:1002022 + label-free proteingroup level quantitation + + + + + Label-free proteingroup level quantitation. + PSI:PI + + + + + + + + + MS2 tag-based analysis. + MS + MS:1002023 + MS2 tag-based analysis + + + + + MS2 tag-based analysis. + PSI:PI + + + + + + + + + + + + + + + MS2 tag-based feature level quantitation. + MS + MS:1002024 + MS2 tag-based feature level quantitation + + + + + MS2 tag-based feature level quantitation. + PSI:PI + + + + + + + + + + + + + + + MS2 tag-based peptide level quantitation. + MS + MS:1002025 + MS2 tag-based peptide level quantitation + + + + + MS2 tag-based peptide level quantitation. + PSI:PI + + + + + + + + + + + + + + + MS2 tag-based protein level quantitation. + MS + MS:1002026 + MS2 tag-based protein level quantitation + + + + + MS2 tag-based protein level quantitation. + PSI:PI + + + + + + + + + + + + + + + MS2 tag-based proteingroup level quantitation. + MS + MS:1002027 + MS2 tag-based proteingroup level quantitation + + + + + MS2 tag-based proteingroup level quantitation. + PSI:PI + + + + + + + + + + + + + + + Nucleic acid base modification (substitution, insertion or deletion). + MS + MS:1002028 + nucleic acid base modification + + + + + Nucleic acid base modification (substitution, insertion or deletion). + PSI:PI + + + + + + + + + + + + + + + Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence. + MS + MS:1002029 + original nucleic acid sequence + + + + + Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence. + PSI:PI + + + + + + + + + + + + + + + Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence. + MS + MS:1002030 + modified nucleic acid sequence + + + + + Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence. + PSI:PI + + + + + + + + + + + + + + + URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment. + MS + MS:1002031 + PASSEL transition group browser URI + + + + + URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment. + PSI:PI + + + + + + + + + + + + + + + URI that allows access to a PeptideAtlas dataset. + MS + MS:1002032 + PeptideAtlas dataset URI + + + + + URI that allows access to a PeptideAtlas dataset. + PSI:PI + + + + + + + + + Role of the contact person. + MS + MS:1002033 + contact role + + + + + Role of the contact person. + PSI:PI + + + + + + + + + The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution. + MS + MS:1002034 + first author + + + + + The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution. + PSI:MS + + + + + + + + + The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution. + MS + MS:1002035 + senior author + + + + + The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution. + PSI:MS + + + + + + + + + One of a set of authors associated with a publication or release. + MS + MS:1002036 + co-author + + + + + One of a set of authors associated with a publication or release. + PSI:MS + + + + + + + + + A person who submits a dataset to a repository. + MS + MS:1002037 + dataset submitter + + + + + A person who submits a dataset to a repository. + PSI:MS + + + + + + + + + A sample that has not been labelled or modified. This is often referred to as "light" to distinguish from "heavy". + light sample + MS + MS:1002038 + label free sample + + + + + A sample that has not been labelled or modified. This is often referred to as "light" to distinguish from "heavy". + PSI:PI + + + + + + + + + + + + + + + Inlet properties that are associated with a value. + MS + MS:1002039 + inlet attribute + + + + + Inlet properties that are associated with a value. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + The temperature of the inlet of a mass spectrometer. + MS + MS:1002040 + inlet temperature + + + + + The temperature of the inlet of a mass spectrometer. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The temperature of the source of a mass spectrometer. + MS + MS:1002041 + source temperature + + + + + The temperature of the source of a mass spectrometer. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column. + MS + MS:1002042 + modulation time + + + + + The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column. + http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429 + + + + + + + + + ProteinProspector software for data acquisition and analysis. + MS + MS:1002043 + ProteinProspector + + + + + ProteinProspector software for data acquisition and analysis. + PSI:PI + + + + + + + + + + + + + + + The ProteinProspector result 'Score'. + MS + MS:1002044 + ProteinProspector:score + + + + + The ProteinProspector result 'Score'. + PSI:PI + + + + + + + + + + + + + + + The ProteinProspector result 'Expectation value'. + MS + MS:1002045 + ProteinProspector:expectation value + + + + + The ProteinProspector result 'Expectation value'. + PSI:PI + + + + + + + + + + + + + + + The original source path used for directory-based sources. + MS + MS:1002046 + native source path + + + + + The original source path used for directory-based sources. + PSI:MS + + + + + + + + + MS-GF software used to re-score the peptide-spectrum matches. + MS + MS:1002047 + MS-GF + + + + + MS-GF software used to re-score the peptide-spectrum matches. + DOI:10.1074/mcp.M110.003731 + PMID:20829449 + + + + + + + + + MS-GF+ software used to analyze the spectra. + MS-GFDB + MS + MS:1002048 + MS-GF+ + + + + + MS-GF+ software used to analyze the spectra. + PSI:PI + + + + + + + + + + + + + + + MS-GF raw score. + MS + MS:1002049 + MS-GF:RawScore + + + + + MS-GF raw score. + PSI:PI + + + + + + + + + + + + + + + MS-GF de novo score. + MS + MS:1002050 + MS-GF:DeNovoScore + + + + + MS-GF de novo score. + PSI:PI + + + + + + + + + + + + + + + MS-GF energy score. + MS + MS:1002051 + MS-GF:Energy + + + + + MS-GF energy score. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + MS-GF spectral E-value. + MS + MS:1002052 + MS-GF:SpecEValue + + + + + MS-GF spectral E-value. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + MS-GF E-value. + MS + MS:1002053 + MS-GF:EValue + + + + + MS-GF E-value. + PSI:PI + + + + + + + + + + + + + + + + MS-GF Q-value. + MS + MS:1002054 + MS-GF:QValue + + + + + MS-GF Q-value. + PSI:PI + + + + + + + + + + + + + + + MS-GF peptide-level Q-value. + MS + MS:1002055 + MS-GF:PepQValue + + + + + MS-GF peptide-level Q-value. + PSI:PI + + + + + + + + + + + + + + + MS-GF posterior error probability. + MS + MS:1002056 + MS-GF:PEP + + + + + MS-GF posterior error probability. + PSI:PI + + + + + + + + + As parameter for search engine: apply the modification only at the N-terminus of a protein. + MS + MS:1002057 + modification specificity protein N-term + + + + + As parameter for search engine: apply the modification only at the N-terminus of a protein. + PSI:PI + + + + + + + + + As parameter for search engine: apply the modification only at the C-terminus of a protein. + MS + MS:1002058 + modification specificity protein C-term + + + + + As parameter for search engine: apply the modification only at the C-terminus of a protein. + PSI:PI + + + + + + + + + Microsoft Excel (can be used for spectral counting). + MS + MS:1002059 + Microsoft Excel + + + + + Microsoft Excel (can be used for spectral counting). + PSI:PI + + + + + + + + + The name of the UniProtKB/TrEMBL database. + MS + MS:1002060 + database UniProtKB/TrEMBL + + + + + The name of the UniProtKB/TrEMBL database. + PSI:PI + + + + + + + + OBSOLETE Decoy database from a TrEMBL protein sequence database. + MS + MS:1002061 + This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. + decoy DB from UniProtKB/TrEMBL + true + + + + + OBSOLETE Decoy database from a TrEMBL protein sequence database. + PSI:PI + + + + + + + + + Metabolic labelling: natural N (mainly 14N). + MS + MS:1002062 + metabolic labelling: natural N (mainly 14N) + + + + + Metabolic labelling: natural N (mainly 14N). + PSI:PI + + + + + + + + + Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite. + MS + MS:1002063 + FindPairs + + + + + Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite. + http://www.medizinisches-proteom-center.de/software + + + + + + + + + + + + + + + Peptide consensus retention time. + MS + MS:1002064 + peptide consensus RT + + + + + Peptide consensus retention time. + PSI:PI + + + + + + + + + + + + + + + Peptide consensus mass/charge ratio. + MS + MS:1002065 + peptide consensus m/z + + + + + Peptide consensus mass/charge ratio. + PSI:PI + + + + + + + + + + + + + + + Method used to calculate the ratio. + MS + MS:1002066 + ratio calculation method + + + + + Method used to calculate the ratio. + PSI:PI + + + + + + + + + + + + + + + Protein quantification value calculated as median of peptide ratios. + MS + MS:1002067 + protein value: median of peptide ratios + + + + + Protein quantification value calculated as median of peptide ratios. + PSI:PI + + + + + + + + + Metabolic labelling: heavy N (mainly 15N). + MS + MS:1002068 + metabolic labelling: heavy N (mainly 15N) + + + + + Metabolic labelling: heavy N (mainly 15N). + PSI:PI + + + + + + + + + + + + + + + Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape. + MS + MS:1002069 + metabolic labelling purity + + + + + Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape. + PSI:PI + + + + + + + + + + + + + + + Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed. + MS + MS:1002070 + t-test + + + + + Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed. + PSI:PI + + + + + + + + + + + + + + + Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed. + MS + MS:1002071 + ANOVA-test + + + + + Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed. + PSI:PI + + + + + + + + + + + + + + + + + + + + + P-value as result of one of the processing steps described. Specify in the description, which processing step it was. + MS + MS:1002072 + p-value + + + + + P-value as result of one of the processing steps described. Specify in the description, which processing step it was. + PSI:PI + + + + + + + + + The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'. + MS + MS:1002073 + mzIdentML format + + + + + The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'. + PSI:PI + http://www.psidev.info/mzidentml + + + + + + + + + File format containing quantification results. + MS + MS:1002074 + quantification file format + + + + + File format containing quantification results. + PSI:PI + + + + + + + + + The mzQuantML format for quantification data from the PSI. File extension '.mzq'. + MS + MS:1002075 + mzQuantML format + + + + + The mzQuantML format for quantification data from the PSI. File extension '.mzq'. + PSI:PI + http://www.psidev.info/mzquantml + + + + + + + + + PAnalyzer software for getting protein evidence categories. + MS + MS:1002076 + PAnalyzer + + + + + PAnalyzer software for getting protein evidence categories. + http://code.google.com/p/ehu-bio/wiki/PAnalyzer + + + + + + + + + Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + MS + MS:1002077 + impact + + + + + Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + PSI:MS + + + + + + + + + + + + + + + OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter. + MS + MS:1002078 + This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. + ProteomeDiscoverer:1. Static Modification + true + + + + + OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter. + MS + MS:1002079 + This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. + ProteomeDiscoverer:2. Static Modification + true + + + + + OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Precursor clipping range before. + MS + MS:1002080 + ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before + + + + + Precursor clipping range before. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Precursor clipping range after. + MS + MS:1002081 + ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After + + + + + Precursor clipping range after. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column. + MS + MS:1002082 + first column elution time + + + + + The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column. + MS + MS:1002083 + second column elution time + + + + + The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column. + PSI:MS + + + + + + + + + Multidimensional chromatography modulation description. + MS + MS:1002084 + multidimensional chromatography modulation description + + + + + Multidimensional chromatography modulation description. + PSI:MS + + + + + + + + + Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition. + MS + MS:1002085 + two-dimensional gas chromatography with fixed modulation time + + + + + Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition. + PSI:MS + + + + + + + + + Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time. + MS + MS:1002086 + two-dimensional gas chromatography with discrete modulation time steps + + + + + Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time. + PSI:MS + + + + + + + + + Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition. + MS + MS:1002087 + two-dimensional liquid chromatography with fixed modulation time + + + + + Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition. + PSI:MS + + + + + + + + + Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time. + MS + MS:1002088 + two-dimensional liquid chromatography with discrete modulation time steps + + + + + Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time. + PSI:MS + + + + + + + + + + + + + + + XCorr threshold for storing peptides that do not belong to a protein. + MS + MS:1002089 + ProteomeDiscoverer:Peptide Without Protein XCorr Threshold + + + + + XCorr threshold for storing peptides that do not belong to a protein. + PSI:MS + + + + + + + + + + + + + + + Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated. + MS + MS:1002090 + Calculate Probability Scores + + + + + Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated. + PSI:MS + + + + + + + + + + + + + + + Delta Cn threshold for filtering out PSM's. + MS + MS:1002091 + ProteomeDiscoverer:Maximum Delta Cn + + + + + Delta Cn threshold for filtering out PSM's. + PSI:MS + + + + + + + + + + + + + + + Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator. + MS + MS:1002092 + Percolator:Validation based on + + + + + Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator. + PSI:MS + + + + + + + + + Search engine input parameter. + MS + MS:1002093 + search engine input parameter + + + + + Search engine input parameter. + PSI:PI + + + + + + + + + Search engine input parameter that is shared by more than one search engine. + MS + MS:1002094 + common search engine input parameter + + + + + Search engine input parameter that is shared by more than one search engine. + PSI:PI + + + + + + + + + Search engine input parameters specific to Mascot. + MS + MS:1002095 + Mascot input parameter + + + + + Search engine input parameters specific to Mascot. + PSI:PI + source:http://www.matrixscience.com/help/search_field_help.html + + + + + + + + + Search engine input parameters specific to SEQUEST. + MS + MS:1002096 + SEQUEST input parameter + + + + + Search engine input parameters specific to SEQUEST. + PSI:PI + source:http://fields.scripps.edu/sequest/parameters.html + + + + + + + + + Search engine input parameters specific to Phenyx. + MS + MS:1002097 + Phenyx input parameter + + + + + Search engine input parameters specific to Phenyx. + PSI:PI + + + + + + + + + Search engine input parameters specific to ProteinExtractor. + MS + MS:1002098 + ProteinExtractor input parameter + + + + + Search engine input parameters specific to ProteinExtractor. + PSI:PI + + + + + + + + + Search engine input parameters specific to OMSSA. + MS + MS:1002099 + OMSSA input parameter + + + + + Search engine input parameters specific to OMSSA. + PSI:PI + + + + + + + + + Search engine input parameters specific to ProteinScape. + MS + MS:1002100 + ProteinScape input parameter + + + + + Search engine input parameters specific to ProteinScape. + PSI:PI + + + + + + + + + Search engine input parameters specific to ProteomeDiscoverer. + MS + MS:1002101 + ProteomeDiscoverer input parameter + + + + + Search engine input parameters specific to ProteomeDiscoverer. + PSI:PI + + + + + + + + + Software input parameters. + MS + MS:1002103 + software input parameter + + + + + Software input parameters. + PSI:PI + + + + + + + + + Software input parameter that is shared by more than one software. + MS + MS:1002104 + common software input parameter + + + + + Software input parameter that is shared by more than one software. + PSI:PI + + + + + + + + + Software specific input parameter. + MS + MS:1002105 + software specific input parameter + + + + + Software specific input parameter. + PSI:PI + + + + + + + + + Search engine input parameters specific to Scaffold. + MS + MS:1002106 + Scaffold input parameter + + + + + Search engine input parameters specific to Scaffold. + PSI:PI + + + + + + + + + Search engine input parameters specific to Percolator. + MS + MS:1002107 + Percolator input parameter + + + + + Search engine input parameters specific to Percolator. + PSI:PI + + + + + + + + + + + + + + Indicates that a higher score is better. + MS + MS:1002108 + higher score better + + + + + Indicates that a higher score is better. + PSI:PI + + + + + + + + + + + + + + Indicates that a lower score is better. + MS + MS:1002109 + lower score better + + + + + Indicates that a lower score is better. + PSI:PI + + + + + + + + + Attribute describing an assay. + MS + MS:1002110 + assay attribute + + + + + Attribute describing an assay. + PSI:PI + + + + + + + + + Attribute describing an assay label. + MS + MS:1002111 + assay label attribute + + + + + Attribute describing an assay label. + PSI:PI + + + + + + + + + Attribute describing a protein group list. + MS + MS:1002112 + protein group list attribute + + + + + Attribute describing a protein group list. + PSI:PI + + + + + + + + + Attribute describing a protein group. + MS + MS:1002113 + protein group attribute + + + + + Attribute describing a protein group. + PSI:PI + + + + + + + + + Attribute describing a protein list. + MS + MS:1002114 + protein list attribute + + + + + Attribute describing a protein list. + PSI:PI + + + + + + + + + Attribute describing a peptide consensus list. + MS + MS:1002115 + peptide consensus list attribute + + + + + Attribute describing a peptide consensus list. + PSI:PI + + + + + + + + + Attribute describing a peptide consensus. + MS + MS:1002116 + peptide consensus attribute + + + + + Attribute describing a peptide consensus. + PSI:PI + + + + + + + + + Attribute describing a small molecule list. + MS + MS:1002117 + small molecule list attribute + + + + + Attribute describing a small molecule list. + PSI:PI + + + + + + + + + Attribute describing a small molecule. + MS + MS:1002118 + small molecule attribute + + + + + Attribute describing a small molecule. + PSI:PI + + + + + + + + + Attribute describing a small molecule modification. + MS + MS:1002119 + small molecule modification attribute + + + + + Attribute describing a small molecule modification. + PSI:PI + + + + + + + + + The name for identifying an experiment. + MS + MS:1002120 + experiment name + + + + + The name for identifying an experiment. + PSI:PI + + + + + + + + + Dummy decribing a spectral count feature. + MS + MS:1002121 + spectral count feature + + + + + Dummy decribing a spectral count feature. + PSI:PI + + + + + + + + + FeatureList of spectral counts. + MS + MS:1002122 + counts reporting + + + + + FeatureList of spectral counts. + PSI:PI + + + + + + + + + X-Tracker generic tool for quantitative proteomics. + MS + MS:1002123 + x-Tracker + + + + + X-Tracker generic tool for quantitative proteomics. + https://bessantlab.org/software/x-tracker/ + + + + + + + + + ProteoSuite software for the analysis of quantitative proteomics data. + MS + MS:1002124 + ProteoSuite + + + + + ProteoSuite software for the analysis of quantitative proteomics data. + DOI:10.1089/omi.2012.0022 + PMID:22804616 + http://www.proteosuite.org/ + + + + + + + + + + + + + + + + OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. + MS + MS:1002125 + This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375). + combined FDRScore + true + + + + + OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. + PMID:19253293 + + + + + + + + + The name of the UniProtKB knowledgebase. + MS + MS:1002126 + database UniProtKB + + + + + The name of the UniProtKB knowledgebase. + PSI:PI + + + + + + + + + Attribute describing an identification file. + MS + MS:1002127 + identification file attribute + + + + + Attribute describing an identification file. + PSI:PI + + + + + + + + + Attribute describing a method file format. + MS + MS:1002128 + method file format + + + + + Attribute describing a method file format. + PSI:PI + + + + + + + + + + Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment. + MS + MS:1002129 + ITRAQAnalyzer + + + + + Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment. + http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP__ITRAQAnalyzer.html + + + + + + + + + Attribute describing an identification file format. + MS + MS:1002130 + identification file format + + + + + Attribute describing an identification file format. + PSI:PI + + + + + + + + + Noise filter component of the TOPP software. + MS + MS:1002131 + TOPP noise filter + + + + + Noise filter component of the TOPP software. + PSI:PI + + + + + + + + + Removes noise from profile spectra by using a gaussian smoothing. + MS + MS:1002132 + TOPP NoiseFilterGaussian + + + + + Removes noise from profile spectra by using a gaussian smoothing. + PSI:PI + + + + + + + + + Removes noise from profile spectra by using a Savitzky-Golay smoothing. + MS + MS:1002133 + TOPP NoiseFilterSGolay + + + + + Removes noise from profile spectra by using a Savitzky-Golay smoothing. + PSI:PI + + + + + + + + + Peak picker component of the TOPP software. + MS + MS:1002134 + TOPP peak picker + + + + + Peak picker component of the TOPP software. + PSI:PI + + + + + + + + + Finds mass spectrometric peaks in high-resoluted profile mass spectra. + MS + MS:1002135 + TOPP PeakPickerHiRes + + + + + Finds mass spectrometric peaks in high-resoluted profile mass spectra. + PSI:PI + + + + + + + + + Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra. + MS + MS:1002136 + TOPP PeakPickerWavelet + + + + + Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra. + PSI:PI + + + + + + + + + Spectra filter component of the TOPP software. + MS + MS:1002137 + TOPP spectra filter + + + + + Spectra filter component of the TOPP software. + PSI:PI + + + + + + + + + Applies a Bern et al normalization to peak spectra. + MS + MS:1002138 + TOPP SpectraFilterBernNorm + + + + + Applies a Bern et al normalization to peak spectra. + DOI:10.1093/bioinformatics/bth947 + PMID:15262780 + + + + + + + + + Applies a filter to peak spectra for marked peaks. + MS + MS:1002139 + TOPP SpectraFilterMarkerMower + + + + + Applies a filter to peak spectra for marked peaks. + PSI:PI + + + + + + + + + Retains the n largest peaks of a peak spectra. + MS + MS:1002140 + TOPP SpectraFilterNLargest + + + + + Retains the n largest peaks of a peak spectra. + PSI:PI + + + + + + + + + Applies a TIC/maximal intensity normalization to peak spectra. + MS + MS:1002141 + TOPP SpectraFilterNormalizer + + + + + Applies a TIC/maximal intensity normalization to peak spectra. + PSI:PI + + + + + + + + + Filters putative unfragmented precursor ions from tandem spectra. + MS + MS:1002142 + TOPP SpectraFilterParentPeakMower + + + + + Filters putative unfragmented precursor ions from tandem spectra. + PSI:PI + + + + + + + + + Applies a filter to peak spectra after intensity scaling according to rank. + MS + MS:1002143 + TOPP SpectraFilterScaler + + + + + Applies a filter to peak spectra after intensity scaling according to rank. + PSI:PI + + + + + + + + + Applies a filter to peak spectra after intensity scaling to the square root. + MS + MS:1002144 + TOPP SpectraFilterSqrtMower + + + + + Applies a filter to peak spectra after intensity scaling to the square root. + PSI:PI + + + + + + + + + Applies a filter of peaks below a given threshold to peak spectra. + MS + MS:1002145 + TOPP SpectraFilterThresholdMower + + + + + Applies a filter of peaks below a given threshold to peak spectra. + PSI:PI + + + + + + + + + Applies a filter of the largest peaks in a sliding window over a peak spectrum. + MS + MS:1002146 + TOPP SpectraFilterWindowMower + + + + + Applies a filter of the largest peaks in a sliding window over a peak spectrum. + PSI:PI + + + + + + + + + Map aligner component of the TOPP software. + MS + MS:1002147 + TOPP map aligner + + + + + Map aligner component of the TOPP software. + PSI:PI + + + + + + + + + Corrects retention time distortions between maps based on common peptide identifications. + MS + MS:1002148 + TOPP MapAlignerIdentification + + + + + Corrects retention time distortions between maps based on common peptide identifications. + PSI:PI + + + + + + + + + Corrects retention time distortions between maps using a pose clustering approach. + MS + MS:1002149 + TOPP MapAlignerPoseClustering + + + + + Corrects retention time distortions between maps using a pose clustering approach. + PSI:PI + + + + + + + + + Corrects retention time distortions between maps by spectrum alignment. + MS + MS:1002150 + TOPP MapAlignerSpectrum + + + + + Corrects retention time distortions between maps by spectrum alignment. + PSI:PI + + + + + + + + + Attribute describing the data type of the numerator of a ratio. + MS + MS:1002151 + numerator data type attribute + + + + + Attribute describing the data type of the numerator of a ratio. + PSI:PI + + + + + + + + + Attribute describing the data type of the denominator of a ratio. + MS + MS:1002152 + denominator data type attribute + + + + + Attribute describing the data type of the denominator of a ratio. + PSI:PI + + + + + + + + + + + + + + + The number of spectra identified for this protein in spectral counting. + MS + MS:1002153 + protein level PSM counts + + + + + The number of spectra identified for this protein in spectral counting. + PSI:PI + + + + + + + + + Extracts spectra of an MS run file to several files in DTA format. + MS + MS:1002154 + TOPP DTAExtractor + + + + + Extracts spectra of an MS run file to several files in DTA format. + PSI:PI + + + + + + + + + Merges several protein/peptide identification files into one file. + MS + MS:1002155 + TOPP IDMerger + + + + + Merges several protein/peptide identification files into one file. + PSI:PI + + + + + + + + + Converts identification engine file formats. + MS + MS:1002156 + TOPP IDFileConverter + + + + + Converts identification engine file formats. + PSI:PI + + + + + + + + + Merges spectra from an LC/MS map, either by precursor or by RT blocks. + MS + MS:1002157 + TOPP SpectraMerger + + + + + Merges spectra from an LC/MS map, either by precursor or by RT blocks. + PSI:PI + + + + + + + + + Exports various XML formats to an mzTab file. + MS + MS:1002158 + TOPP MzTabExporter + + + + + Exports various XML formats to an mzTab file. + PSI:PI + + + + + + + + + Annotates mass traces in centroided LC/MS maps. + MS + MS:1002159 + TOPP MassTraceExtractor + + + + + Annotates mass traces in centroided LC/MS maps. + PSI:PI + + + + + + + + + Correct the precursor entries of tandem MS scans. + MS + MS:1002160 + TOPP PrecursorMassCorrector + + + + + Correct the precursor entries of tandem MS scans. + PSI:PI + + + + + + + + + Performs precursor mz correction on centroided high resolution data. + MS + MS:1002161 + TOPP HighResPrecursorMassCorrector + + + + + Performs precursor mz correction on centroided high resolution data. + PSI:PI + + + + + + + + + Computes an additive series to quantify a peptide in a set of samples. + MS + MS:1002162 + TOPP AdditiveSeries + + + + + Computes an additive series to quantify a peptide in a set of samples. + PSI:PI + + + + + + + + + Decharges and merges different feature charge variants of the same chemical entity. + MS + MS:1002163 + TOPP Decharger + + + + + Decharges and merges different feature charge variants of the same chemical entity. + PSI:PI + + + + + + + + + Quantifies signals at given positions in (raw or picked) LC/MS maps. + MS + MS:1002164 + TOPP EICExtractor + + + + + Quantifies signals at given positions in (raw or picked) LC/MS maps. + PSI:PI + + + + + + + + + Feature finder component of the TOPP software. + MS + MS:1002165 + TOPP feature finder + + + + + Feature finder component of the TOPP software. + PSI:PI + + + + + + + + + Detects two-dimensional features in centroided LC-MS data. + MS + MS:1002166 + TOPP FeatureFinderCentroided + + + + + Detects two-dimensional features in centroided LC-MS data. + PSI:PI + + + + + + + + + Detects two-dimensional features in uncentroided LC-MS data. + MS + MS:1002167 + TOPP FeatureFinderRaw + + + + + Detects two-dimensional features in uncentroided LC-MS data. + PSI:PI + + + + + + + + + Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm. + MS + MS:1002168 + TOPP FeatureFinderIsotopeWavelet + + + + + Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm. + PSI:PI + + + + + + + + + Detects two-dimensional features in centroided LC-MS data of metabolites. + MS + MS:1002169 + TOPP FeatureFinderMetabo + + + + + Detects two-dimensional features in centroided LC-MS data of metabolites. + PSI:PI + + + + + + + + + Quantifies features LC-MS/MS MRM data. + MS + MS:1002170 + TOPP FeatureFinderMRM + + + + + Quantifies features LC-MS/MS MRM data. + PSI:PI + + + + + + + + + Computes protein abundances from annotated feature/consensus maps. + MS + MS:1002171 + TOPP ProteinQuantifier + + + + + Computes protein abundances from annotated feature/consensus maps. + PSI:PI + + + + + + + + + Normalizes maps of one consensus XML file (after linking). + MS + MS:1002172 + TOPP ConsensusMapNormalizer + + + + + Normalizes maps of one consensus XML file (after linking). + PSI:PI + + + + + + + + + Applies retention time transformations to maps. + MS + MS:1002173 + TOPP MapRTTransformer + + + + + Applies retention time transformations to maps. + PSI:PI + + + + + + + + + Feature linker component of the TOPP software. + MS + MS:1002174 + TOPP feature linker + + + + + Feature linker component of the TOPP software. + PSI:PI + + + + + + + + + Groups corresponding isotope-labeled features in a feature map. + MS + MS:1002175 + TOPP FeatureLinkerLabeled + + + + + Groups corresponding isotope-labeled features in a feature map. + PSI:PI + + + + + + + + + Groups corresponding features from multiple maps. + MS + MS:1002176 + TOPP FeatureLinkerUnlabeled + + + + + Groups corresponding features from multiple maps. + PSI:PI + + + + + + + + + Groups corresponding features from multiple maps using a quality threshold clustering approach. + MS + MS:1002177 + TOPP FeatureLinkerUnlabeledQT + + + + + Groups corresponding features from multiple maps using a quality threshold clustering approach. + PSI:PI + + + + + + + + + Performs a peptide/protein identification with the CompNovo engine. + MS + MS:1002178 + TOPP CompNovo + + + + + Performs a peptide/protein identification with the CompNovo engine. + PSI:PI + + + + + + + + + Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode. + MS + MS:1002179 + TOPP CompNovoCID + + + + + Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode. + PSI:PI + + + + + + + + + Software adaptor to an external program in the TOPP software. + MS + MS:1002180 + TOPP software adaptor + + + + + Software adaptor to an external program in the TOPP software. + PSI:PI + + + + + + + + + Identifies MS2 spectra using the external program Inspect. + MS + MS:1002181 + TOPP InspectAdapter + + + + + Identifies MS2 spectra using the external program Inspect. + PSI:PI + + + + + + + + + Identifies MS2 spectra using the external program Mascot. + MS + MS:1002182 + TOPP MascotAdapter + + + + + Identifies MS2 spectra using the external program Mascot. + PSI:PI + + + + + + + + + Identifies MS2 spectra using the online version of the external program Mascot. + MS + MS:1002183 + TOPP MascotAdapterOnline + + + + + Identifies MS2 spectra using the online version of the external program Mascot. + PSI:PI + + + + + + + + + Identifies MS2 spectra using the external program OMSSA. + MS + MS:1002184 + TOPP OMSSAAdapter + + + + + Identifies MS2 spectra using the external program OMSSA. + PSI:PI + + + + + + + + + Identifies MS2 spectra using the external program PepNovo. + MS + MS:1002185 + TOPP PepNovoAdapter + + + + + Identifies MS2 spectra using the external program PepNovo. + PSI:PI + + + + + + + + + Identifies MS2 spectra using the external program XTandem. + MS + MS:1002186 + TOPP XTandemAdapter + + + + + Identifies MS2 spectra using the external program XTandem. + PSI:PI + + + + + + + + + Identifies peptide MS2 spectra by spectral matching with a searchable spectral library. + MS + MS:1002187 + TOPP SpecLibSearcher + + + + + Identifies peptide MS2 spectra by spectral matching with a searchable spectral library. + PSI:PI + + + + + + + + + Computes a consensus identification from peptide identifications of several identification engines. + MS + MS:1002188 + TOPP ConsensusID + + + + + Computes a consensus identification from peptide identifications of several identification engines. + PSI:PI + + + + + + + + + Resolves ambiguous annotations of features with peptide identifications. + MS + MS:1002189 + TOPP IDConflictResolver + + + + + Resolves ambiguous annotations of features with peptide identifications. + PSI:PI + + + + + + + + + Filters results from protein or peptide identification engines based on different criteria. + MS + MS:1002190 + TOPP IDFilter + + + + + Filters results from protein or peptide identification engines based on different criteria. + PSI:PI + + + + + + + + + Assigns protein/peptide identifications to feature or consensus features. + MS + MS:1002191 + TOPP IDMapper + + + + + Assigns protein/peptide identifications to feature or consensus features. + PSI:PI + + + + + + + + + Estimates posterior error probabilities using a mixture model. + MS + MS:1002192 + TOPP IDPosteriorErrorProbability + + + + + Estimates posterior error probabilities using a mixture model. + PSI:PI + + + + + + + + + Calibrate Retention times of peptide hits to standards. + MS + MS:1002193 + TOPP IDRTCalibration + + + + + Calibrate Retention times of peptide hits to standards. + PSI:PI + + + + + + + + + Refreshes the protein references for all peptide hits. + MS + MS:1002194 + TOPP PeptideIndexer + + + + + Refreshes the protein references for all peptide hits. + PSI:PI + + + + + + + + + A tool for precursor ion selection based on identification results. + MS + MS:1002195 + TOPP PrecursorIonSelector + + + + + A tool for precursor ion selection based on identification results. + PSI:PI + + + + + + + + + MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML). + MS + MS:1002196 + TOPP MRMMapper + + + + + MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML). + PSI:PI + + + + + + + + + OpenSwath component of the TOPP software. + MS + MS:1002197 + TOPP OpenSwath component + + + + + OpenSwath component of the TOPP software. + PSI:PI + + + + + + + + + Picks peaks and finds features in an SRM experiment. + MS + MS:1002198 + TOPP OpenSwathAnalyzer + + + + + Picks peaks and finds features in an SRM experiment. + PSI:PI + + + + + + + + + Extract chromatograms (XIC) from a MS2 map file. + MS + MS:1002199 + TOPP OpenSwathChromatogramExtractor + + + + + Extract chromatograms (XIC) from a MS2 map file. + PSI:PI + + + + + + + + + Generates decoys according to different models for a specific TraML. + MS + MS:1002200 + TOPP OpenSwathDecoyGenerator + + + + + Generates decoys according to different models for a specific TraML. + PSI:PI + + + + + + + + + Converts a featureXML to a mProphet tsv (tab separated values). + MS + MS:1002201 + TOPP OpenSwathFeatureXMLToTSV + + + + + Converts a featureXML to a mProphet tsv (tab separated values). + PSI:PI + + + + + + + + + Generates a transformation file for retention time space into normalized space. + MS + MS:1002202 + TOPP OpenSwathRTNormalizer + + + + + Generates a transformation file for retention time space into normalized space. + PSI:PI + + + + + + + + + Infer proteins from a list of (high-confidence) peptides. + MS + MS:1002203 + TOPP ProteinInference + + + + + Infer proteins from a list of (high-confidence) peptides. + PSI:PI + + + + + + + + + Estimates the false discovery rate on peptide and protein level using decoy searches. + MS + MS:1002204 + TOPP FalseDiscoveryRate + + + + + Estimates the false discovery rate on peptide and protein level using decoy searches. + PSI:PI + + + + + + + + + Converts, filters, and processes mass spectrometry data in variety of formats. + MS + MS:1002205 + ProteoWizard msconvert + + + + + Converts, filters, and processes mass spectrometry data in variety of formats. + PSI:MS + + + + + + + + + Converts, filters, and processes identifications from shotgun proteomics experiments. + MS + MS:1002206 + ProteoWizard idconvert + + + + + Converts, filters, and processes identifications from shotgun proteomics experiments. + PSI:MS + + + + + + + + + Filters and processes protein sequence databases. + MS + MS:1002207 + ProteoWizard chainsaw + + + + + Filters and processes protein sequence databases. + PSI:MS + + + + + + + + + Filters, processes, and displays mass spectrometry data in a variety of ways. + MS + MS:1002208 + ProteoWizard msaccess + + + + + Filters, processes, and displays mass spectrometry data in a variety of ways. + PSI:MS + + + + + + + + + An interactive GUI application to view and filter mass spectrometry data in a variety of formats. + MS + MS:1002209 + ProteoWizard SeeMS + + + + + An interactive GUI application to view and filter mass spectrometry data in a variety of formats. + PSI:MS + + + + + + + + + + A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data. + MS + MS:1002210 + IsobariQ + + + + + A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data. + DOI:10.1021/pr1009977 + PMID:21067241 + http://folk.uio.no/magnusar/isobariq + + + + + + + + + The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. + MS + MS:1002211 + Variance stabilizing normalization + + + + + The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. + PMID:16646781 + + + + + + + + + Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric. + MS + MS:1002212 + IPTL quantitation analysis + + + + + Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric. + PMID:19655813 + PSI:PI + + + + + + + + + + + + + + + A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum). + MS + MS:1002213 + PAnalyzer:conclusive protein + + + + + A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum). + PSI:PI + + + + + + + + + + + + + + + A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum). + MS + MS:1002214 + PAnalyzer:indistinguishable protein + + + + + A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum). + PSI:PI + + + + + + + + + + + + + + + A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). + MS + MS:1002215 + PAnalyzer:non-conclusive protein + + + + + A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). + PSI:PI + + + + + + + + + + + + + + + A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). + MS + MS:1002216 + PAnalyzer:ambiguous group member + + + + + A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum). + PSI:PI + + + + + + + + + + + + + + + A putative identified peptide issued from a decoy sequence database. + MS + MS:1002217 + decoy peptide + + + + + A putative identified peptide issued from a decoy sequence database. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion. + MS + MS:1002218 + percent collision energy ramp start + + + + + Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion. + MS + MS:1002219 + percent collision energy ramp end + + + + + Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion. + PSI:PI + + + + + + + + + A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database. + MS + MS:1002220 + MRMaid + + + + + A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database. + PSI:PI + + + + + + + + + + Score in MRMaid to indicate the expected performance of the peptide in SRM. + MS + MS:1002221 + MRMaid:peptide score + + + + + Score in MRMaid to indicate the expected performance of the peptide in SRM. + PSI:PI + + + + + + + + + + + + + + + Attribute associated with a SRM transition. + MS + MS:1002222 + SRM transition attribute + + + + + Attribute associated with a SRM transition. + PSI:MS + + + + + + + + + + + + + + + Probability of detecting precursor when parent protein is present. + MS + MS:1002223 + precursor ion detection probability + + + + + Probability of detecting precursor when parent protein is present. + PSI:PI + + + + + + + + + + + + + + + Probability of detecting product ion when precursor ion is present. + MS + MS:1002224 + product ion detection probability + + + + + Probability of detecting product ion when precursor ion is present. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Average value of product ion intensity in a collection of identified spectra. + MS + MS:1002225 + average product ion intensity + + + + + Average value of product ion intensity in a collection of identified spectra. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Standard deviation of product ion intensity in a collection of identified spectra. + MS + MS:1002226 + product ion intensity standard deviation + + + + + Standard deviation of product ion intensity in a collection of identified spectra. + PSI:PI + + + + + + + + + + + + + + + The number of times the specific product ion has been observed in a series of SRM experiments. + MS + MS:1002227 + number of product ion observations + + + + + The number of times the specific product ion has been observed in a series of SRM experiments. + PSI:PI + + + + + + + + + + + + + + + The number of times the specific precursor ion has been observed in a series of SRM experiments. + MS + MS:1002228 + number of precursor ion observations + + + + + The number of times the specific precursor ion has been observed in a series of SRM experiments. + PSI:PI + + + + + + + + + + + + + + + Calculated relaxed significance when performing a decoy search for high-confidence peptides. + MS + MS:1002229 + ProteomeDiscoverer:Mascot:Significance Middle + + + + + Calculated relaxed significance when performing a decoy search for high-confidence peptides. + PSI:PI + + + + + + + + + + + + + + + Calculated relaxed significance when performing a decoy search for medium-confidence peptides. + MS + MS:1002230 + ProteomeDiscoverer:Mascot:Significance High + + + + + Calculated relaxed significance when performing a decoy search for medium-confidence peptides. + PSI:PI + + + + + + + + + ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12}). + MS + MS:1002231 + regular expressions for a GUID + + + + + ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12}). + PSI:PI + + + + + + + + + + + + + + + The default FDR calculator as globally unique identifier (GUID). + MS + MS:1002232 + ProteomeDiscoverer:Default FDR calculator + + + + + The default FDR calculator as globally unique identifier (GUID). + PSI:PI + + + + + + + + + + + + + + + Flag indicating if low-resolution spectra are taken into consideration. + MS + MS:1002233 + ProteomeDiscoverer:SEQUEST:Low resolution spectra contained + + + + + Flag indicating if low-resolution spectra are taken into consideration. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Mass-to-charge ratio of a precursor ion selected for fragmentation. + MS + selected ion m/z + MS:1002234 + selected precursor m/z + + + + + Mass-to-charge ratio of a precursor ion selected for fragmentation. + PSI:PI + + + + + + + + + + + + + + + A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores. + MS + MS:1002235 + ProteoGrouper:PDH score + + + + + A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores. + PSI:PI + + + + + + + + + + + + + + + A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides. + MS + MS:1002236 + ProteoGrouper:PAG score + + + + + A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides. + PSI:PI + + + + + + + + + A library of Java routines for manipulating mzIdentML files. + MS + MS:1002237 + mzidLib + + + + + A library of Java routines for manipulating mzIdentML files. + PSI:PI + + + + + + + + + A converter for OMSSA OMX to mzIdentML. + MS + MS:1002238 + mzidLib:Omssa2Mzid + + + + + A converter for OMSSA OMX to mzIdentML. + PSI:PI + + + + + + + + + A converter for Tandem XML to mzIdentML. + MS + MS:1002239 + mzidLib:Tandem2Mzid + + + + + A converter for Tandem XML to mzIdentML. + PSI:PI + + + + + + + + + A converter for CSV files (following OMSSA CSV style) to mzIdentML. + MS + MS:1002240 + mzidLib:Csv2Mzid + + + + + A converter for CSV files (following OMSSA CSV style) to mzIdentML. + PSI:PI + + + + + + + + + A generic and parameterizable protein inference algorithm for mzIdentML files. + MS + MS:1002241 + mzidLib:ProteoGrouper + + + + + A generic and parameterizable protein inference algorithm for mzIdentML files. + PSI:PI + + + + + + + + + A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files. + MS + MS:1002242 + mzidLib:Thresholder + + + + + A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files. + PSI:PI + + + + + + + + + A routine for adding emPAI quantitative values to an mzIdentML file. + MS + MS:1002243 + mzidLib:Perform emPAI on mzid + + + + + A routine for adding emPAI quantitative values to an mzIdentML file. + PSI:PI + + + + + + + + + A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search. + MS + MS:1002244 + mzidLib:FalseDiscoveryRate + + + + + A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search. + PSI:PI + + + + + + + + + A tool for converting mzIdentML files to CSV format. + MS + MS:1002245 + mzidLib:Mzidentml2Csv + + + + + A tool for converting mzIdentML files to CSV format. + PSI:PI + + + + + + + + + A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file. + MS + MS:1002246 + mzidLib:CombineSearchEngines + + + + + A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file. + PMID:19253293 + + + + + + + + + A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files. + MS + MS:1002247 + mzidLib:InsertMetaDataFromFasta + + + + + A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'SpScore'. + MS + MS:1002248 + SEQUEST:spscore + + + + + The SEQUEST result 'SpScore'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'SpRank'. + MS + MS:1002249 + SEQUEST:sprank + + + + + The SEQUEST result 'SpRank'. + PSI:PI + + + + + + + + + + + + + + + The SEQUEST result 'DeltaCnStar'. + MS + MS:1002250 + SEQUEST:deltacnstar + + + + + The SEQUEST result 'DeltaCnStar'. + PSI:PI + + + + + + + + + Comet open-source sequence search engine developed at the University of Washington. + MS + MS:1002251 + Comet + + + + + Comet open-source sequence search engine developed at the University of Washington. + PMID:23148064 + + + + + + + + + + + + + + + + + + + + + The Comet result 'XCorr'. + MS + MS:1002252 + Comet:xcorr + + + + + The Comet result 'XCorr'. + PSI:PI + + + + + + + + + + + + + + + The Comet result 'DeltaCn'. + MS + MS:1002253 + Comet:deltacn + + + + + The Comet result 'DeltaCn'. + PSI:PI + + + + + + + + + + + + + + + The Comet result 'DeltaCnStar'. + MS + MS:1002254 + Comet:deltacnstar + + + + + The Comet result 'DeltaCnStar'. + PSI:PI + + + + + + + + + + + + + + + The Comet result 'SpScore'. + MS + MS:1002255 + Comet:spscore + + + + + The Comet result 'SpScore'. + PSI:PI + + + + + + + + + + + + + + + The Comet result 'SpRank'. + MS + MS:1002256 + Comet:sprank + + + + + The Comet result 'SpRank'. + PSI:PI + + + + + + + + + + + + + + + The Comet result 'Expectation value'. + MS + MS:1002257 + Comet:expectation value + + + + + The Comet result 'Expectation value'. + PSI:PI + + + + + + + + + + + + + + + The Comet result 'Matched Ions'. + MS + MS:1002258 + Comet:matched ions + + + + + The Comet result 'Matched Ions'. + PSI:PI + + + + + + + + + + + + + + + The Comet result 'Total Ions'. + MS + MS:1002259 + Comet:total ions + + + + + The Comet result 'Total Ions'. + PSI:PI + + + + + + + + + + + + + + + False-discovery rate threshold for peptide-spectrum matches. + MS + MS:1002260 + PSM:FDR threshold + + + + + False-discovery rate threshold for peptide-spectrum matches. + PSI:PI + + + + + + + + + Byonic search engine from Protein Metrics. + MS + MS:1002261 + Byonic + + + + + Byonic search engine from Protein Metrics. + PMID:23255153 + + + + + + + + + + + + + + + + + + + + + The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct. + MS + MS:1002262 + Byonic:Score + + + + + The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct. + MS + MS:1002263 + Byonic:Delta Score + + + + + The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct. + MS + MS:1002264 + Byonic:DeltaMod Score + + + + + The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Byonic posterior error probability. + MS + MS:1002265 + Byonic:PEP + + + + + Byonic posterior error probability. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism. + MS + MS:1002266 + Byonic:Peptide LogProb + + + + + The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The log p-value of the protein. + MS + MS:1002267 + Byonic:Protein LogProb + + + + + The log p-value of the protein. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + Best (most negative) log p-value of an individual PSM. + MS + MS:1002268 + Byonic:Best LogProb + + + + + Best (most negative) log p-value of an individual PSM. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Best (largest) Byonic score of a PSM. + MS + MS:1002269 + Byonic:Best Score + + + + + Best (largest) Byonic score of a PSM. + PSI:PI + + + + + + + + + A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure. + MS + MS:1002270 + chromatography separation + + + + + A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure. + PSI:MS + + + + + + + + + Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid. + MS + MS:1002271 + liquid chromatography separation + + + + + Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid. + PSI:MS + + + + + + + + + Gas chromatography (GC) is a separation technique in which the mobile phase is a gas. + MS + MS:1002272 + gas chromatography separation + + + + + Gas chromatography (GC) is a separation technique in which the mobile phase is a gas. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Detector potential difference in volts. + MS + MS:1002273 + detector potential + + + + + Detector potential difference in volts. + PSI:MS + + + + + + + + + Waters quadrupole based SQ Detector 2. + MS + MS:1002274 + SQ Detector 2 + + + + + Waters quadrupole based SQ Detector 2. + PSI:MS + + + + + + + + + Waters oa-ToF based Xevo G2-S Tof. + MS + MS:1002275 + Xevo G2-S Tof + + + + + Waters oa-ToF based Xevo G2-S Tof. + PSI:MS + + + + + + + + + Waters oa-ToF based Xevo G2-S QTof. + MS + MS:1002276 + Xevo G2-S QTof + + + + + Waters oa-ToF based Xevo G2-S QTof. + PSI:MS + + + + + + + + + Waters AutoSpec Premier magnetic sector instrument. + MS + MS:1002277 + AutoSpec Premier + + + + + Waters AutoSpec Premier magnetic sector instrument. + PSI:MS + + + + + + + + + LECO nominal mass resolution time-of-flight GC mass spectrometer. + MS + MS:1002278 + Pegasus III + + + + + LECO nominal mass resolution time-of-flight GC mass spectrometer. + PSI:MS + + + + + + + + + Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + MS + MS:1002279 + maXis 4G + + + + + Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + PSI:MS + + + + + + + + + Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + MS + MS:1002280 + compact + + + + + Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + PSI:MS + + + + + + + + + Selected Reaction Monitoring feature level quantitation. + MS + MS:1002281 + SRM feature level quantitation + + + + + Selected Reaction Monitoring feature level quantitation. + PSI:PI + + + + + + + + + Selected Reaction Monitoring peptide level quantitation. + MS + MS:1002282 + SRM peptide level quantitation + + + + + Selected Reaction Monitoring peptide level quantitation. + PSI:PI + + + + + + + + + Selected Reaction Monitoring protein level quantitation. + MS + MS:1002283 + SRM protein level quantitation + + + + + Selected Reaction Monitoring protein level quantitation. + PSI:PI + + + + + + + + + Selected Reaction Monitoring proteingroup level quantitation. + MS + MS:1002284 + SRM proteingroup level quantitation + + + + + Selected Reaction Monitoring proteingroup level quantitation. + PSI:PI + + + + + + + + + A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology. + TPP + MS + MS:1002285 + Trans-Proteomic Pipeline + + + + + A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology. + PSI:PI + + + + + + + + + + + + + + + A software program that is a component of the Trans-Proteomic Pipeline. + MS + MS:1002286 + Trans-Proteomic Pipeline software + + + + + A software program that is a component of the Trans-Proteomic Pipeline. + PSI:PI + + + + + + + + + A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format. + MS + MS:1002287 + PeptideProphet + + + + + A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format. + PMID:12403597 + PMID:23176103 + + + + + + + + + A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format. + InterProphet + MS + MS:1002288 + iProphet + + + + + A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format. + PMID:21876204 + + + + + + + + + A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format. + MS + MS:1002289 + ProteinProphet + + + + + A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format. + PMID:14632076 + + + + + + + + + A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. + MS + MS:1002290 + XPRESS + + + + + A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. + PSI:PI + + + + + + + + + A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc. + MS + MS:1002291 + Libra + + + + + A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc. + PSI:PI + + + + + + + + + A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites. + MS + MS:1002292 + PTMProphet + + + + + A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites. + PSI:PI + + + + + + + + + Bruker Daltonics' SCION series. + MS + MS:1002293 + Bruker Daltonics SCION series + + + + + Bruker Daltonics' SCION series. + PSI:MS + + + + + + + + + Bruker Daltonics' EVOQ series. + MS + MS:1002294 + Bruker Daltonics EVOQ series + + + + + Bruker Daltonics' EVOQ series. + PSI:MS + + + + + + + + + Bruker Daltonics' SCION SQ: GC-single quadrupole. + MS + MS:1002295 + SCION SQ + + + + + Bruker Daltonics' SCION SQ: GC-single quadrupole. + PSI:MS + + + + + + + + + Bruker Daltonics' SCION TQ: GC-triple quadrupole. + MS + MS:1002296 + SCION TQ + + + + + Bruker Daltonics' SCION TQ: GC-triple quadrupole. + PSI:MS + + + + + + + + + Bruker Daltonics' EVOQ Elite: LC-triple quadrupole. + MS + MS:1002297 + EVOQ Elite + + + + + Bruker Daltonics' EVOQ Elite: LC-triple quadrupole. + PSI:MS + + + + + + + + + Bruker Daltonics' EVOQ Qube: LC-triple quadrupole. + MS + MS:1002298 + EVOQ Qube + + + + + Bruker Daltonics' EVOQ Qube: LC-triple quadrupole. + PSI:MS + + + + + + + + + Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + MS + MS:1002299 + micrOTOF-Q III + + + + + Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + PSI:MS + + + + + + + + + Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray. + MS + MS:1002300 + amaZon Speed ETD + + + + + Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray. + PSI:MS + + + + + + + + + Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + MS + MS:1002301 + amaZon Speed + + + + + Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray. + PSI:MS + + + + + + + + + Bruker Container raw file format. + MS + MS:1002302 + Bruker Container format + + + + + Bruker Container raw file format. + PSI:MS + + + + + + + + + + + + + + + Native identifier (UUID). + MS + MS:1002303 + Bruker Container nativeID format + + + + + Native identifier (UUID). + PSI:MS + + + + + + + + + + + + + + Domain range of a numerical value. + MS + MS:1002304 + domain range + + + + + Domain range of a numerical value. + PSI:PI + + + + + + + + + Value range for probabilities. + MS + MS:1002305 + value between 0 and 1 inclusive + + + + + Value range for probabilities. + PSI:PI + + + + + + + + + Positive value range. + MS + MS:1002306 + value greater than zero + + + + + Positive value range. + PSI:PI + + + + + + + + + Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion. + MS + MS:1002307 + fragmentation ion type + + + + + Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion. + PSI:PI + + + + + + + + + A detector using a fluorescent signal after excitation with light. + MS + MS:1002308 + fluorescence detector + + + + + A detector using a fluorescent signal after excitation with light. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM. + MS + MS:1002309 + Byonic: Peptide AbsLogProb + + + + + The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein. + MS + MS:1002310 + Byonic: Protein AbsLogProb + + + + + The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information. + MS + MS:1002311 + Byonic: Peptide AbsLogProb2D + + + + + The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information. + PSI:PI + + + + + + + + + Compression using MS-Numpress linear prediction compression. + MS + MS:1002312 + MS-Numpress linear prediction compression + + + + + Compression using MS-Numpress linear prediction compression. + https://github.com/ms-numpress/ms-numpress + + + + + + + + + Compression using MS-Numpress positive integer compression. + MS + MS:1002313 + MS-Numpress positive integer compression + + + + + Compression using MS-Numpress positive integer compression. + https://github.com/ms-numpress/ms-numpress + + + + + + + + + Compression using MS-Numpress short logged float compression. + MS + MS:1002314 + MS-Numpress short logged float compression + + + + + Compression using MS-Numpress short logged float compression. + https://github.com/ms-numpress/ms-numpress + + + + + + + + + Indicates a consensus result from several search engine runs. + MS + MS:1002315 + consensus result + + + + + Indicates a consensus result from several search engine runs. + PSI:PI + + + + + + + + + + + + + + + Strict confidence probability score. + MS + MS:1002316 + ProteomeDiscoverer:Amanda:high confidence threshold + + + + + Strict confidence probability score. + PSI:PI + + + + + + + + + + + + + + + Relaxed confidence probability score. + MS + MS:1002317 + ProteomeDiscoverer:Amanda:middle confidence threshold + + + + + Relaxed confidence probability score. + PSI:PI + + + + + + + + + + + + + + + Flag indicating automatic estimation of the workload level. + MS + MS:1002318 + ProteomeDiscoverer:automatic workload + + + + + Flag indicating automatic estimation of the workload level. + PSI:PI + + + + + + + + + + + + + + + The Amanda score of the scoring function for a PSM. + MS + MS:1002319 + Amanda:AmandaScore + + + + + The Amanda score of the scoring function for a PSM. + PSI:PI + + + + + + + + + + + + + + + Maximum dynamic modifications per PSM. + MS + MS:1002320 + ProteomeDiscoverer:max differential modifications + + + + + Maximum dynamic modifications per PSM. + PSI:PI + + + + + + + + + + + + + + + Maximum equal modifications per PSM. + MS + MS:1002321 + ProteomeDiscoverer:max equal modifications + + + + + Maximum equal modifications per PSM. + PSI:PI + + + + + + + + + + + + + + + Minimum peptide length. + MS + MS:1002322 + ProteomeDiscoverer:min peptide length + + + + + Minimum peptide length. + PSI:PI + + + + + + + + + + + + + + + Maximum peptide length. + MS + MS:1002323 + ProteomeDiscoverer:max peptide length + + + + + Maximum peptide length. + PSI:PI + + + + + + + + + + + + + + + Maximum number of same neutral losses. + MS + MS:1002324 + ProteomeDiscoverer:max number neutral loss + + + + + Maximum number of same neutral losses. + PSI:PI + + + + + + + + + + + + + + + Max number of same neutral losses of modifications. + MS + MS:1002325 + ProteomeDiscoverer:max number neutral loss modifications + + + + + Max number of same neutral losses of modifications. + PSI:PI + + + + + + + + + + + + + + + Flag for usage of flanking ions. + MS + MS:1002326 + ProteomeDiscoverer:use flanking ions + + + + + Flag for usage of flanking ions. + PSI:PI + + + + + + + + + + + + + + + The maximum number of possible equal modifications per PSM. + MS + MS:1002327 + ProteomeDiscoverer:max number of same modifs + + + + + The maximum number of possible equal modifications per PSM. + PSI:PI + + + + + + + + + + + + + + + Defines whether a simple deisotoping shall be performed. + MS + MS:1002328 + ProteomeDiscoverer:perform deisotoping + + + + + Defines whether a simple deisotoping shall be performed. + PSI:PI + + + + + + + + + + + + + + + Specifies the fragment ions and neutral losses that are calculated. + MS + MS:1002329 + ProteomeDiscoverer:ion settings + + + + + Specifies the fragment ions and neutral losses that are calculated. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter. + MS + MS:1002330 + This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. + ProteomeDiscoverer:3. Static Modification + true + + + + + OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter. + MS + MS:1002331 + This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. + ProteomeDiscoverer:5. Dynamic Modification + true + + + + + OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter. + PSI:PI + + + + + + + + + The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group. + MS + MS:1002332 + lab head + + + + + The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group. + PSI:PI + + + + + + + + + Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process. + MS + MS:1002333 + conversion software + + + + + Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process. + PSI:PI + + + + + + + + + Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML. + MS + MS:1002334 + ProCon + + + + + Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML. + PSI:PI + http://www.medizinisches-proteom-center.de/procon + + + + + + + + + Java software designed to convert one of several proteomics identification results formats into PRIDE XML. + MS + MS:1002335 + PRIDE Converter2 + + + + + Java software designed to convert one of several proteomics identification results formats into PRIDE XML. + PMID:22949509 + + + + + + + + + Amanda scoring system for PSM identification. + MS + MS:1002336 + Amanda + + + + + Amanda scoring system for PSM identification. + PSI:PI + + + + + + + + + Andromeda is a peptide search engine. + MS + MS:1002337 + Andromeda + + + + + Andromeda is a peptide search engine. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The probability based score of the Andromeda search engine. + MS + MS:1002338 + Andromeda:score + + + + + The probability based score of the Andromeda search engine. + PSI:PI + + + + + + + + + + + + + + + Estimation of global false discovery rate of peptides with a post-translational modification. + MS + MS:1002339 + site:global FDR + + + + + Estimation of global false discovery rate of peptides with a post-translational modification. + PSI:PI + + + + + + + + + + + + + + + Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project. + MS + MS:1002340 + ProteomeXchange project tag + + + + + Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project. + PSI:PI + + + + + + + + + + + + + + + A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search. + MS + MS:1002341 + second-pass peptide identification + + + + + A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search. + PSI:PI + + + + + + + + + + A framework for differential analysis of mass spectrometry data. + MS + MS:1002342 + MZmine + + + + + A framework for differential analysis of mass spectrometry data. + PMID:16403790 + PMID:20650010 + + + + + + + + OBSOLETE Stability type of the ion. + MS + MS:1002343 + This child of the former purgatory term ion was made obsolete. + ion stability type + true + + + + + OBSOLETE Stability type of the ion. + PSI:PI + + + + + + + + + + Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers. + MS + MS:1002344 + Maltcms + + + + + Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers. + PSI:PI + http://maltcms.sf.net + + + + + + + + + + + + + + + Attribute of a single peptide-spectrum match. + MS + MS:1002345 + PSM-level attribute + + + + + Attribute of a single peptide-spectrum match. + PSI:PI + + + + + + + + + Protein group level information. + MS + MS:1002346 + protein group-level identification attribute + + + + + Protein group level information. + PSI:PI + + + + + + + + + Identification confidence metric for a peptide spectrum match. + MS + MS:1002347 + PSM-level identification statistic + + + + + Identification confidence metric for a peptide spectrum match. + PSI:PI + + + + + + + + + Identification confidence metric for a protein group. + MS + MS:1002348 + protein group-level identification statistic + + + + + Identification confidence metric for a protein group. + PSI:PI + + + + + + + + + Positive value range less than or equal to 1. + MS + MS:1002349 + value greater than zero but less than or equal to one + + + + + Positive value range less than or equal to 1. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the global false discovery rate of peptide spectrum matches. + MS + MS:1002350 + PSM-level global FDR + + + + + Estimation of the global false discovery rate of peptide spectrum matches. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the local false discovery rate of peptide spectrum matches. + MS + MS:1002351 + PSM-level local FDR + + + + + Estimation of the local false discovery rate of peptide spectrum matches. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the p-value for peptide spectrum matches. + MS + MS:1002352 + PSM-level p-value + + + + + Estimation of the p-value for peptide spectrum matches. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the e-value for peptide spectrum matches. + MS + MS:1002353 + PSM-level e-value + + + + + Estimation of the e-value for peptide spectrum matches. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the q-value for peptide spectrum matches. + MS + MS:1002354 + PSM-level q-value + + + + + Estimation of the q-value for peptide spectrum matches. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + mzidLibrary FDRScore for peptide spectrum matches. + MS + MS:1002355 + PSM-level FDRScore + + + + + mzidLibrary FDRScore for peptide spectrum matches. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. + MS + MS:1002356 + PSM-level combined FDRScore + + + + + mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum. + MS + MS:1002357 + PSM-level probability + + + + + Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum. + PSI:PI + + + + + + + + + Search engine specific distinct peptide score. + MS + MS:1002358 + search engine specific peptide sequence-level identification statistic + + + + + Search engine specific distinct peptide score. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + MS + MS:1002359 + peptide sequence-level local FDR + + + + + Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + PSI:PI + + + + + + + + + + + + + + + + + + + + + + MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + MS + MS:1002360 + distinct peptide-level FDRScore + + + + + MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + PSI:PI + + + + + + + + + + + + + + + + + + + + + + Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools. + MS + MS:1002361 + distinct peptide-level combined FDRScore + + + + + Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs. + MS + MS:1002362 + peptide sequence-level probability + + + + + Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs. + PSI:PI + + + + + + + + + Search engine specific protein scores. + MS + MS:1002363 + search engine specific score for proteins + + + + + Search engine specific protein scores. + PSI:PI + + + + + + + + + + + + + + + Estimation of the local false discovery rate of proteins. + MS + MS:1002364 + protein-level local FDR + + + + + Estimation of the local false discovery rate of proteins. + PSI:PI + + + + + + + + + + + + + + + + + + + + + MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. + MS + MS:1002365 + FDRScore for proteins + + + + + MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. + PSI:PI + + + + + + + + + + + + + + + + + + + + + MzidLibrary Combined FDRScore for proteins. + MS + MS:1002366 + combined FDRScore for proteins + + + + + MzidLibrary Combined FDRScore for proteins. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. + MS + MS:1002367 + probability for proteins + + + + + Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. + PSI:PI + + + + + + + + + Search engine specific protein group scores. + MS + MS:1002368 + search engine specific score for protein groups + + + + + Search engine specific protein group scores. + PSI:PI + + + + + + + + + + + + + + + Estimation of the global false discovery rate of protein groups. + MS + MS:1002369 + protein group-level global FDR + + + + + Estimation of the global false discovery rate of protein groups. + PSI:PI + + + + + + + + + + + + + + + Estimation of the local false discovery rate of protein groups. + MS + MS:1002370 + protein group-level local FDR + + + + + Estimation of the local false discovery rate of protein groups. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the p-value for protein groups. + MS + MS:1002371 + protein group-level p-value + + + + + Estimation of the p-value for protein groups. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the e-value for protein groups. + MS + MS:1002372 + protein group-level e-value + + + + + Estimation of the e-value for protein groups. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the q-value for protein groups. + MS + MS:1002373 + protein group-level q-value + + + + + Estimation of the q-value for protein groups. + PSI:PI + + + + + + + + + + + + + + + + + + + + + mzidLibrary FDRScore for protein groups. + MS + MS:1002374 + protein group-level FDRScore + + + + + mzidLibrary FDRScore for protein groups. + PSI:PI + + + + + + + + + + + + + + + + + + + + + mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. + MS + MS:1002375 + protein group-level combined FDRScore + + + + + mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools. + PMID:19253293 + + + + + + + + + + + + + + + + + + + + + Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. + MS + MS:1002376 + protein group-level probability + + + + + Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software. + PSI:PI + + + + + + + + + + + + + + + Specifies the threshold value for relaxed scoring. + MS + MS:1002377 + ProteomeDiscoverer:Relaxed Score Threshold + + + + + Specifies the threshold value for relaxed scoring. + PSI:PI + + + + + + + + + + + + + + + Specifies the threshold value for strict scoring. + MS + MS:1002378 + ProteomeDiscoverer:Strict Score Threshold + + + + + Specifies the threshold value for strict scoring. + PSI:PI + + + + + + + + + + + + + + + Cut off score for storing peptides that do not belong to a protein. + MS + MS:1002379 + ProteomeDiscoverer:Peptide Without Protein Cut Off Score + + + + + Cut off score for storing peptides that do not belong to a protein. + PSI:PI + + + + + + + + + + + + + + + Estimation of the false localization rate for modification site assignment. + MS + MS:1002380 + false localization rate + + + + + Estimation of the false localization rate for modification site assignment. + PSI:PI + + + + + + + + + + + + Software for automated LC-MALDI analysis and reporting. + MS + MS:1002381 + MALDI Solutions LC-MALDI + + + + + Software for automated LC-MALDI analysis and reporting. + PSI:PI + + + + + + + + + Shimadzu MALDI-7090: MALDI-TOF-TOF. + MS + MS:1002382 + Shimadzu MALDI-7090 + + + + + Shimadzu MALDI-7090: MALDI-TOF-TOF. + PSI:PI + + + + + + + + + SCiLS software for data acquisition and analysis. + MS + MS:1002383 + SCiLS software + + + + + SCiLS software for data acquisition and analysis. + PSI:MS + + + + + + + + + + + SCiLS Lab software. + MS + MS:1002384 + SCiLS Lab + + + + + SCiLS Lab software. + PSI:MS + + + + + + + + + SCiLS Lab file format. + MS + MS:1002385 + SCiLS Lab format + + + + + SCiLS Lab file format. + PSI:MS + + + + + + + + + Preprocessing software. + MS + MS:1002386 + preprocessing software + + + + + Preprocessing software. + PSI:PI + + + + + + + + + + PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis. + MS + MS:1002387 + PIA + + + + + PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis. + PSI:PI + http://www.medizinisches-proteom-center.de/pia + + + + + + + + + A compilation of search engine results in the PIA XML format. + MS + MS:1002388 + PIA XML format + + + + + A compilation of search engine results in the PIA XML format. + PSI:PI + + + + + + + + + + A parameter set for a single PIA analysis. + MS + MS:1002389 + PIA workflow parameter + + + + + A parameter set for a single PIA analysis. + PSI:PI + + + + + + + + + + + + + + + Indicates whether the FDR score was calculated for the input file. + MS + MS:1002390 + PIA:FDRScore calculated + + + + + Indicates whether the FDR score was calculated for the input file. + PSI:PI + + + + + + + + + + + + + + + Indicates whether the combined FDR score was calculated for the PIA compilation. + MS + MS:1002391 + PIA:Combined FDRScore calculated + + + + + Indicates whether the combined FDR score was calculated for the PIA compilation. + PSI:PI + + + + + + + + + + + + + + + Indicates whether PSM sets were created. + MS + MS:1002392 + PIA:PSM sets created + + + + + Indicates whether PSM sets were created. + PSI:PI + + + + + + + + + + + + + + + The number of top identifications per spectrum used for the FDR calculation, 0 means all. + MS + MS:1002393 + PIA:used top identifications for FDR + + + + + The number of top identifications per spectrum used for the FDR calculation, 0 means all. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The score given to a protein by any protein inference. + MS + MS:1002394 + PIA:protein score + + + + + The score given to a protein by any protein inference. + PSI:PI + + + + + + + + + + + + + + + The used algorithm for the protein inference using PIA. + MS + MS:1002395 + PIA:protein inference + + + + + The used algorithm for the protein inference using PIA. + PSI:PI + + + + + + + + + + + + + + + A filter used by PIA for the protein inference. + MS + MS:1002396 + PIA:protein inference filter + + + + + A filter used by PIA for the protein inference. + PSI:PI + + + + + + + + + + + + + + + The used scoring method for the protein inference using PIA. + MS + MS:1002397 + PIA:protein inference scoring + + + + + The used scoring method for the protein inference using PIA. + PSI:PI + + + + + + + + + + + + + + + The used base score for the protein inference using PIA. + MS + MS:1002398 + PIA:protein inference used score + + + + + The used base score for the protein inference using PIA. + PSI:PI + + + + + + + + + + + + + + + The method to determine the PSMs used for scoring by the protein inference. + MS + MS:1002399 + PIA:protein inference used PSMs + + + + + The method to determine the PSMs used for scoring by the protein inference. + PSI:PI + + + + + + + + + + + + + + + A filter used for the report generation. + MS + MS:1002400 + PIA:filter + + + + + A filter used for the report generation. + PSI:PI + + + + + + + + + At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members. + MS + MS:1002401 + leading protein + + + + + At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members. + PSI:PI + + + + + + + + + Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence. + MS + MS:1002402 + non-leading protein + + + + + Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence. + PSI:PI + + + + + + + + + An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative. + MS + MS:1002403 + group representative + + + + + An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file. + MS + MS:1002404 + count of identified proteins + + + + + The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file. + PSI:PI + + + + + + + + + Details describing a protein cluster. + MS + MS:1002405 + protein group-level result list attribute + + + + + Details describing a protein cluster. + PSI:PI + + + + + + + + + + + + + + + The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. + MS + MS:1002406 + count of identified clusters + + + + + The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. + DOI:10.1002/pmic.201400080 + PMID:25092112 + + + + + + + + + + + + + + + An identifier applied to protein groups to indicate that they are linked by shared peptides. + MS + MS:1002407 + cluster identifier + + + + + An identifier applied to protein groups to indicate that they are linked by shared peptides. + PSI:PI + + + + + + + + + + + + + + + The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. + MS + MS:1002408 + number of distinct protein sequences + + + + + The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file. + PSI:PI + + + + + + + + + Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group. + MS + MS:1002409 + marginally distinguished protein + + + + + Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group. + PSI:PI + + + + + + + + + + Anubis software for selected reaction monitoring data. + MS + MS:1002410 + Anubis + + + + + Anubis software for selected reaction monitoring data. + PSI:PI + http://quantitativeproteomics.org/anubis + + + + + + + + + The TraML format for transitions in SRM from the PSI. File extension '.TraML'. + MS + MS:1002411 + TraML format + + + + + The TraML format for transitions in SRM from the PSI. File extension '.TraML'. + PSI:PI + http://www.psidev.info/traml + + + + + + + + + + + + + + + Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM). + MS + MS:1002412 + total XIC area + + + + + Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM). + PSI:PI + + + + + + + + + + + + + + + The background area for the quantified transition. + MS + MS:1002413 + product background + + + + + The background area for the quantified transition. + PSI:PI + + + + + + + + + Postprocessing software. + MS + MS:1002414 + postprocessing software + + + + + Postprocessing software. + PSI:PI + + + + + + + + + + + + + + + A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file. + MS + MS:1002415 + protein group passes threshold + + + + + A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file. + PSI:PI + + + + + + + + + Thermo Scientific Orbitrap Fusion. + MS + MS:1002416 + Orbitrap Fusion + + + + + Thermo Scientific Orbitrap Fusion. + PSI:PI + + + + + + + + + Thermo Scientific Orbitrap Fusion with ETD. + MS + MS:1002417 + Orbitrap Fusion ETD + + + + + Thermo Scientific Orbitrap Fusion with ETD. + PSI:PI + + + + + + + + + Thermo Scientific TSQ Quantiva MS. + MS + MS:1002418 + TSQ Quantiva + + + + + Thermo Scientific TSQ Quantiva MS. + PSI:PI + + + + + + + + + Thermo Scientific TSQ Endura MS. + MS + MS:1002419 + TSQ Endura + + + + + Thermo Scientific TSQ Endura MS. + PSI:PI + + + + + + + + + + + + + + + URI that allows access to a PASSEL experiment. + MS + MS:1002420 + PASSEL experiment URI + + + + + URI that allows access to a PASSEL experiment. + PSI:PI + + + + + + + + + Search engine input parameters specific to Paragon. + MS + MS:1002421 + Paragon input parameter + + + + + Search engine input parameters specific to Paragon. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation. + MS + MS:1002422 + Paragon: sample type + + + + + The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation. + MS + MS:1002423 + Paragon: cysteine alkylation + + + + + The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument. + MS + MS:1002424 + Paragon: instrument setting + + + + + The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search. + MS + MS:1002425 + Paragon: search effort + + + + + The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search. + PSI:PI + + + + + + + + + + + + + + + A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions. + MS + MS:1002426 + Paragon: ID focus + + + + + A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting that controls whether FDR analysis is conducted. + MS + MS:1002427 + Paragon: FDR analysis + + + + + The Paragon method setting that controls whether FDR analysis is conducted. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting that controls whether quantitation analysis is conducted. + MS + MS:1002428 + Paragon: quantitation + + + + + The Paragon method setting that controls whether quantitation analysis is conducted. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples. + MS + MS:1002429 + Paragon: background correction + + + + + The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity. + MS + MS:1002430 + Paragon: bias correction + + + + + The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity. + PSI:PI + + + + + + + + + + + + + + + The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios. + MS + MS:1002431 + Paragon: channel to use as denominator in ratios + + + + + The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios. + PSI:PI + + + + + + + + + Search engine specific metadata that are not user-controlled settings. + MS + MS:1002432 + search engine specific input metadata + + + + + Search engine specific metadata that are not user-controlled settings. + PSI:PI + + + + + + + + + + + + + + + This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result. + MS + MS:1002433 + Paragon: modified data dictionary or parameter translation + + + + + This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result. + PSI:PI + + + + + + + + + + + + + + + Number of spectra in a search. + MS + MS:1002434 + number of spectra searched + + + + + Number of spectra in a search. + PSI:PI + + + + + + + + + + + + + + + The time that a data processing action was started. + MS + MS:1002435 + data processing start time + + + + + The time that a data processing action was started. + PSI:MS + + + + + + + + + + + + + + + The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done. + MS + MS:1002436 + Paragon: digestion + + + + + The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done. + PSI:PI + + + + + + + + + + + + + + + The number of decoy sequences, if the concatenated target-decoy approach is used. + MS + MS:1002437 + number of decoy sequences + + + + + The number of decoy sequences, if the concatenated target-decoy approach is used. + PSI:PI + + + + + + + + + + + + + + Information about the list of PSMs (SpectrumIdentificationList). + MS + MS:1002438 + spectrum identification list result details + + + + + Information about the list of PSMs (SpectrumIdentificationList). + PSI:PI + + + + + + + + + A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult. + MS + MS:1002439 + final PSM list + + + + + A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult. + PSI:PI + + + + + + + + + A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult. + MS + MS:1002440 + intermediate PSM list + + + + + A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult. + PSI:PI + + + + + + + + + AIA Analytical Data Interchange file format for mass spectrometry data. + MS + MS:1002441 + Andi-MS format + + + + + AIA Analytical Data Interchange file format for mass spectrometry data. + PSI:PI + + + + + + + + + The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. + MS + MS:1002442 + chromatograph file format + + + + + The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format. + PSI:PI + + + + + + + + + AIA Analytical Data Interchange file format for chromatography data. + MS + MS:1002443 + Andi-CHROM format + + + + + AIA Analytical Data Interchange file format for chromatography data. + PSI:PI + + + + + + + + + The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1002444 + 6420 Triple Quadrupole LC/MS + + + + + The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity. + MS + MS:1002445 + 6460 Triple Quadrupole LC/MS + + + + + The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity. + PSI:MS + + + + + + + + + The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity. + MS + MS:1002446 + 6490 Triple Quadrupole LC/MS + + + + + The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity. + PSI:MS + + + + + + + + + + + + + + + The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects. + MS + MS:1002447 + Paragon:special factor + + + + + The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects. + PSI:PI + + + + + + + + + + + + + + + The PEAKS inChorus peptide score. + MS + MS:1002448 + PEAKS:inChorusPeptideScore + + + + + The PEAKS inChorus peptide score. + PSI:PI + + + + + + + + + + + + + + + The PEAKS inChorus protein score. + MS + MS:1002449 + PEAKS:inChorusProteinScore + + + + + The PEAKS inChorus protein score. + PSI:PI + + + + + + + + + Ion b-H3PO4: b ion with lost phosphoric acid. + MS + MS:1002450 + param: b ion-H3PO4 DEPRECATED + + + + + Ion b-H3PO4: b ion with lost phosphoric acid. + PSI:PI + + + + + + + + + Ion y-H3PO4: y ion with lost phosphoric acid. + MS + MS:1002451 + param: y ion-H3PO4 DEPRECATED + + + + + Ion y-H3PO4: y ion with lost phosphoric acid. + PSI:PI + + + + + + + + + + The Maltcms Graphical User Interface. + MS + MS:1002452 + Maui + + + + + The Maltcms Graphical User Interface. + PSI:PI + http://maltcms.sf.net + + + + + + + + + No fixed modifications are included as a parameter for the search, and therefore they are not reported. + MS + MS:1002453 + No fixed modifications searched + + + + + No fixed modifications are included as a parameter for the search, and therefore they are not reported. + PSI:PI + + + + + + + + + No variable modifications are included as a parameter for the search, and therefore they are not reported. + MS + MS:1002454 + No variable modifications searched + + + + + No variable modifications are included as a parameter for the search, and therefore they are not reported. + PSI:PI + + + + + + + + + + OBSOLETE Neutral loss of water. + MS + MS:1002455 + This term was obsoleted because it should be replaced by MS:1000336 with value H2O. + H2O neutral loss + true + + + + + OBSOLETE Neutral loss of water. + PSI:PI + + + + + + + + + + OBSOLETE Neutral loss of ammonia. + MS + MS:1002456 + This term was obsoleted because it should be replaced by MS:1000336 with value NH3. + NH3 neutral loss + true + + + + + OBSOLETE Neutral loss of ammonia. + PSI:PI + + + + + + + + + + OBSOLETE Neutral loss of phosphoric acid. + MS + MS:1002457 + This term was obsoleted because it should be replaced by MS:1000336 with value H3PO4. + H3PO4 neutral loss + true + + + + + OBSOLETE Neutral loss of phosphoric acid. + PSI:PI + + + + + + + + + PeptideShaker is a software for the interpretation of proteomics identification results. + MS + MS:1002458 + PeptideShaker + + + + + PeptideShaker is a software for the interpretation of proteomics identification results. + PSI:PI + http://peptide-shaker.googlecode.com + + + + + + + + + MS Amanda csv output format. + MS + MS:1002459 + MS Amanda csv format + + + + + MS Amanda csv output format. + PSI:PI + + + + + + + + + + + + + + + Estimation of the global false negative rate of protein groups. + MS + MS:1002460 + protein group-level global FNR + + + + + Estimation of the global false negative rate of protein groups. + PSI:PI + + + + + + + + + Estimation of the global confidence of protein groups. + MS + MS:1002461 + protein group-level confidence + + + + + Estimation of the global confidence of protein groups. + PSI:PI + + + + + + + + + + + + + + + Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + MS + MS:1002462 + peptide sequence-level global FNR + + + + + Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + PSI:PI + + + + + + + + + Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + MS + MS:1002463 + peptide sequence-level global confidence + + + + + Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry). + PSI:PI + + + + + + + + + + + + + + + Estimation of the global false negative rate of peptide spectrum matches. + MS + MS:1002464 + PSM-level global FNR + + + + + Estimation of the global false negative rate of peptide spectrum matches. + PSI:PI + + + + + + + + + Estimation of the global confidence of peptide spectrum matches. + MS + MS:1002465 + PSM-level global confidence + + + + + Estimation of the global confidence of peptide spectrum matches. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The probability based PeptideShaker PSM score. + MS + MS:1002466 + PeptideShaker PSM score + + + + + The probability based PeptideShaker PSM score. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The probability based PeptideShaker PSM confidence. + MS + MS:1002467 + PeptideShaker PSM confidence + + + + + The probability based PeptideShaker PSM confidence. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + The probability based PeptideShaker peptide score. + MS + MS:1002468 + PeptideShaker peptide score + + + + + The probability based PeptideShaker peptide score. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The probability based PeptideShaker peptide confidence. + MS + MS:1002469 + PeptideShaker peptide confidence + + + + + The probability based PeptideShaker peptide confidence. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + The probability based PeptideShaker protein group score. + MS + MS:1002470 + PeptideShaker protein group score + + + + + The probability based PeptideShaker protein group score. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The probability based PeptideShaker protein group confidence. + MS + MS:1002471 + PeptideShaker protein group confidence + + + + + The probability based PeptideShaker protein group confidence. + PSI:PI + + + + + + + + + A collision-induced dissociation process that occurs in a trap-type collision cell. + MS + MS:1002472 + trap-type collision-induced dissociation + + + + + A collision-induced dissociation process that occurs in a trap-type collision cell. + PSI:PI + + + + + + + + + The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine. + MS + MS:1002473 + ion series considered in search + + + + + The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group. + MS + MS:1002474 + ProteoAnnotator:non-canonical gene model score + + + + + The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group. + PSI:PI + + + + + + + + + + + + + + + The count of the number of peptide sequences mapped to non-canonical gene models only within the group. + MS + MS:1002475 + ProteoAnnotator:count alternative peptides + + + + + The count of the number of peptide sequences mapped to non-canonical gene models only within the group. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated. + MS + MS:1002476 + ion mobility drift time + + + + + Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1002477 + mean ion mobility drift time array + + + + + Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum. + binary-data-type:MS:1000521 + MS + MS:1002478 + mean charge array + + + + + Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + + + + + + + + + + Regular expression. + MS + MS:1002479 + regular expression + + + + + Regular expression. + PSI:PI + + + + + + + + + (10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&'<>])[^ +\r +\v\f])+). + MS + MS:1002480 + regular expression for a digital object identifier (DOI) + + + + + (10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&'<>])[^ +\r +\v\f])+). + PSI:PI + http://dx.doi.org/ + + + + + + + + + A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV. + MS + MS:1002481 + higher energy beam-type collision-induced dissociation + + + + + A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV. + PSI:MS + + + + + + + + + Estimated statistical threshold. + MS + MS:1002482 + statistical threshold + + + + + Estimated statistical threshold. + PSI:MS + + + + + + + + + Estimated statistical threshold at PSM-level. + MS + MS:1002483 + PSM-level statistical threshold + + + + + Estimated statistical threshold at PSM-level. + PSI:MS + + + + + + + + + Estimated statistical threshold at peptide-level. + MS + MS:1002484 + peptide-level statistical threshold + + + + + Estimated statistical threshold at peptide-level. + PSI:MS + + + + + + + + + Estimated statistical threshold at protein-level. + MS + MS:1002485 + protein-level statistical threshold + + + + + Estimated statistical threshold at protein-level. + PSI:MS + + + + + + + + + Estimated statistical threshold at protein group-level. + MS + MS:1002486 + protein group-level statistical threshold + + + + + Estimated statistical threshold at protein group-level. + PSI:PI + + + + + + + + + + + + + + + Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + MS + MS:1002487 + MassIVE dataset identifier + + + + + Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + PSI:PI + + + + + + + + + + + + + + + URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + MS + MS:1002488 + MassIVE dataset URI + + + + + URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + PSI:PI + + + + + + + + + + + + + + + Details describing a special processing. + MS + MS:1002489 + special processing + + + + + Details describing a special processing. + PSI:PI + + + + + + + + + Peptide-level scoring performed. + MS + MS:1002490 + peptide-level scoring + + + + + Peptide-level scoring performed. + PSI:PI + + + + + + + + + Modification localization scoring performed. + MS + MS:1002491 + modification localization scoring + + + + + Modification localization scoring performed. + PSI:PI + + + + + + + + + Consensus multiple search engine approach performed. + MS + MS:1002492 + consensus scoring + + + + + Consensus multiple search engine approach performed. + PSI:PI + + + + + + + + + Sample pre-fractionation performed. + MS + MS:1002493 + sample pre-fractionation + + + + + Sample pre-fractionation performed. + PSI:PI + + + + + + + + + Cross-linking search performed. + MS + MS:1002494 + cross-linking search + + + + + Cross-linking search performed. + PSI:PI + + + + + + + + + No special processing performed. + MS + MS:1002495 + no special processing + + + + + No special processing performed. + PSI:PI + + + + + + + + + Group PSMs by distinct peptide sequence ignoring modifications. + MS + MS:1002496 + group PSMs by sequence + + + + + Group PSMs by distinct peptide sequence ignoring modifications. + PSI:PI + + + + + + + + + Group PSMs by distinct peptide sequence with taking modifications into account. + MS + MS:1002497 + group PSMs by sequence with modifications + + + + + Group PSMs by distinct peptide sequence with taking modifications into account. + PSI:PI + + + + + + + + + Group PSMs by distinct peptide sequence with taking modifications and charge into account. + MS + MS:1002498 + group PSMs by sequence with modifications and charge + + + + + Group PSMs by distinct peptide sequence with taking modifications and charge into account. + PSI:PI + + + + + + + + + OBSOLETE Peptide level score. + MS + MS:1002499 + This term was obsoleted because it was never intended to go in the CV. + peptide level score + true + + + + + OBSOLETE Peptide level score. + PSI:PI + + + + + + + + + + + + + + + A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file. + MS + MS:1002500 + peptide passes threshold + + + + + A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file. + PSI:PI + + + + + + + + + Indicating that no PSM threshold was used. + MS + MS:1002501 + no PSM threshold + + + + + Indicating that no PSM threshold was used. + PSI:PI + + + + + + + + + Indicating that no peptide-level threshold was used. + MS + MS:1002502 + no peptide-level threshold + + + + + Indicating that no peptide-level threshold was used. + PSI:PI + + + + + + + + + Flags a PSM that it is used for peptide-level scoring. + MS + MS:1002503 + PSM is used for peptide-level scoring + + + + + Flags a PSM that it is used for peptide-level scoring. + PSI:PI + + + + + + + + + + + + + + + The order of modifications to be referenced elsewhere in the document. + MS + MS:1002504 + modification index + + + + + The order of modifications to be referenced elsewhere in the document. + PSI:PI + + + + + + + + + ([:digit:]+:[0|1]{1}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]{1}[:digit:]+:(true|false){1}). + MS + MS:1002505 + regular expression for modification localization scoring + + + + + ([:digit:]+:[0|1]{1}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]{1}[:digit:]+:(true|false){1}). + PSI:PI + + + + + + + + + Modification position score. + MS + MS:1002506 + modification position score + + + + + Modification position score. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Mod position score: false localization rate. + MS + MS:1002507 + modification rescoring:false localization rate + + + + + Mod position score: false localization rate. + PSI:PI + + + + + + + + + Cross-linking attribute. + MS + MS:1002508 + cross-linking attribute + + + + + Cross-linking attribute. + PSI:PI + + + + + + + + + + + + + + + The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. + MS + MS:1002509 + cross-link donor + + + + + The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. + PSI:PI + + + + + + + + + + + + + + + Cross-linking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. + MS + MS:1002510 + cross-link acceptor + + + + + Cross-linking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. + PSI:PI + + + + + + + + + + + + + + + Cross-linked spectrum identification item. + MS + MS:1002511 + cross-link spectrum identification item + + + + + Cross-linked spectrum identification item. + PSI:PI + + + + + + + + + + + + + + + Cross-linking scoring value. + MS + MS:1002512 + cross-linking score + + + + + Cross-linking scoring value. + PSI:PI + + + + + + + + + + + + + + + The absolute abundance of protein in a cell. + MS + MS:1002513 + molecules per cell + + + + + The absolute abundance of protein in a cell. + PSI:PI + + + + + + + + + Absolute quantitation analysis. + MS + MS:1002514 + absolute quantitation analysis + + + + + Absolute quantitation analysis. + PSI:PI + + + + + + + + + + + + + + + States whether an internal peptide reference is used or not in absolute quantitation analysis. + MS + MS:1002515 + internal peptide reference used + + + + + States whether an internal peptide reference is used or not in absolute quantitation analysis. + PSI:PI + + + + + + + + + + + + + + + States whether an internal protein reference is used or not in absolute quantitation analysis. + MS + MS:1002516 + internal protein reference used + + + + + States whether an internal protein reference is used or not in absolute quantitation analysis. + PSI:PI + + + + + + + + + + + + + + + The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis. + MS + MS:1002517 + internal reference abundance + + + + + The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis. + PSI:PI + + + + + + + + + + + + + + + The data type normalised abundance for protein groups produced by Progenesis LC-MS. + MS + MS:1002518 + Progenesis:protein group normalised abundance + + + + + The data type normalised abundance for protein groups produced by Progenesis LC-MS. + PSI:PI + + + + + + + + + + + + + + + The data type raw abundance for protein groups produced by Progenesis LC-MS. + MS + MS:1002519 + Progenesis:protein group raw abundance + + + + + The data type raw abundance for protein groups produced by Progenesis LC-MS. + PSI:PI + + + + + + + + + + + + + + + Peptide group identifier for peptide-level stats. + MS + MS:1002520 + peptide group ID + + + + + Peptide group identifier for peptide-level stats. + PSI:PI + + + + + + + + + A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position. + MS + MS:1002521 + mass spectrometry imaging + + + + + A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position. + PSI:PI + + + + + + + + + + + + + + + Determine 1st static terminal post-translational modifications (PTMs). + MS + MS:1002522 + ProteomeDiscoverer:1. Static Terminal Modification + + + + + Determine 1st static terminal post-translational modifications (PTMs). + PSI:PI + + + + + + + + + Thermo Scientific Q Exactive. + MS + MS:1002523 + Q Exactive HF + + + + + Thermo Scientific Q Exactive. + PSI:PI + + + + + + + + + Thermo Scientific PepFinder BioPharma analysis software. + MS + MS:1002524 + PepFinder + + + + + Thermo Scientific PepFinder BioPharma analysis software. + PSI:PI + + + + + + + + + Thermo Scientific TSQ 8000 Evo MS. + MS + MS:1002525 + TSQ 8000 Evo + + + + + Thermo Scientific TSQ 8000 Evo MS. + PSI:PI + + + + + + + + + Thermo Scientific Exactive Plus MS. + MS + MS:1002526 + Exactive Plus + + + + + Thermo Scientific Exactive Plus MS. + PSI:PI + + + + + + + + + Instrument specific scan properties that are associated with a value. + MS + MS:1002527 + instrument specific scan attribute + + + + + Instrument specific scan properties that are associated with a value. + PSI:PI + + + + + + + + + Synchronous prefilter selection. + SPS + MS + MS:1002528 + synchronous prefilter selection + + + + + Synchronous prefilter selection. + PSI:PI + + + + + + + + + A data array of resolution values. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1002529 + resolution array + + + + + A data array of resolution values. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + A data array of signal baseline values (the signal in the absence of analytes). + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1002530 + baseline array + + + + + A data array of signal baseline values (the signal in the absence of analytes). + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data. + MS + MS:1002531 + UIMF format + + + + + SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data. + PSI:MS + + + + + + + + + Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger. + MS + MS:1002532 + UIMF nativeID format + + + + + Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer. + MS + MS:1002533 + TripleTOF 6600 + + + + + SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer. + PSI:MS + + + + + + + + + + + + + + + + + + + + + The ProLuCID result 'XCorr'. + MS + MS:1002534 + ProLuCID:xcorr + + + + + The ProLuCID result 'XCorr'. + PSI:PI + + + + + + + + + + + + + + + The ProLuCID result 'DeltaCn'. + MS + MS:1002535 + ProLuCID:deltacn + + + + + The ProLuCID result 'DeltaCn'. + PSI:PI + + + + + + + + + + + + + + + + + + + + + D-Score for PTM site location at the PSM-level. + MS + MS:1002536 + D-Score + + + + + D-Score for PTM site location at the PSM-level. + PMID:23307401 + + + + + + + + + + + + + + + + + + + + + MD-Score for PTM site location at the PSM-level. + MS + MS:1002537 + MD-Score + + + + + MD-Score for PTM site location at the PSM-level. + PMID:21057138 + + + + + + + + + + + + + + + Localization confidence metric for a post translational modification (PTM). + MS + MS:1002538 + PTM localization confidence metric + + + + + Localization confidence metric for a post translational modification (PTM). + PSI:PI + + + + + + + + + + + + + + + PeptideShaker quality criteria for the confidence of PTM localizations. + MS + MS:1002539 + PeptideShaker PTM confidence type + + + + + PeptideShaker quality criteria for the confidence of PTM localizations. + PSI:PI + + + + + + + + + + + + + + + PeptideShaker quality criteria for the confidence of PSM's. + MS + MS:1002540 + PeptideShaker PSM confidence type + + + + + PeptideShaker quality criteria for the confidence of PSM's. + PSI:PI + + + + + + + + + + + + + + + PeptideShaker quality criteria for the confidence of peptide identifications. + MS + MS:1002541 + PeptideShaker peptide confidence type + + + + + PeptideShaker quality criteria for the confidence of peptide identifications. + PSI:PI + + + + + + + + + + + + + + + PeptideShaker quality criteria for the confidence of protein identifications. + MS + MS:1002542 + PeptideShaker protein confidence type + + + + + PeptideShaker quality criteria for the confidence of protein identifications. + PSI:PI + + + + + + + + + Target/Decoy based FDR estimation for cross-linking peptide-identifications. + MS + MS:1002543 + xiFDR + + + + + Target/Decoy based FDR estimation for cross-linking peptide-identifications. + PSI:PI + + + + + + + + + Search engine for cross-linked peptides. + MS + MS:1002544 + xi + + + + + Search engine for cross-linked peptides. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The xi result 'Score'. + MS + MS:1002545 + xi:score + + + + + The xi result 'Score'. + PSI:PI + + + + + + + + + + A software package to convert Skyline report to mzQuantML. + MS + MS:1002546 + Skyline mzQuantML converter + + + + + A software package to convert Skyline report to mzQuantML. + PSI:PI + http://code.google.com/p/srm-mzquantml-convertor/ + + + + + + + + + A normalized spectral abundance factor (NSAF). + MS + MS:1002547 + normalized spectral abundance factor + + + + + A normalized spectral abundance factor (NSAF). + DOI:10.1021/pr060161n + PMID:16944946 + + + + + + + + + A distributed normalized spectral abundance factor (dNSAF). + MS + MS:1002548 + distributed normalized spectral abundance factor + + + + + A distributed normalized spectral abundance factor (dNSAF). + DOI:10.1021/ac9023999 + PMID:20166708 + + + + + + + + + Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence. + MS + MS:1002549 + PTM localization distinct peptide-level statistic + + + + + Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence. + PSI:PI + + + + + + + + + + + + + + + + + + + + + phosphoRS score for PTM site location at the peptide-level. + MS + MS:1002550 + peptide:phosphoRS score + + + + + phosphoRS score for PTM site location at the peptide-level. + PSI:PI + + + + + + + + + + + + + + + + + + + + + A-score for PTM site location at the peptide-level. + MS + MS:1002551 + peptide:Ascore + + + + + A-score for PTM site location at the peptide-level. + PSI:PI + + + + + + + + + + + + + + + + + + + + + H-Score for peptide phosphorylation site location at the peptide-level. + MS + MS:1002552 + peptide:H-Score + + + + + H-Score for peptide phosphorylation site location at the peptide-level. + PSI:PI + + + + + + + + + + + + + + + + + + + + + D-Score for PTM site location at the peptide-level. + MS + MS:1002553 + peptide:D-Score + + + + + D-Score for PTM site location at the peptide-level. + PSI:PI + + + + + + + + + + + + + + + + + + + + + MD-Score for PTM site location at the peptide-level. + MS + MS:1002554 + peptide:MD-Score + + + + + MD-Score for PTM site location at the peptide-level. + PSI:PI + + + + + + + + + Threshold for PTM site location score. + MS + MS:1002555 + PTM localization score threshold + + + + + Threshold for PTM site location score. + PSI:PI + + + + + + + + + + + + + + + Threshold for Ascore PTM site location score. + MS + MS:1002556 + Ascore threshold + + + + + Threshold for Ascore PTM site location score. + PSI:PI + + + + + + + + + + + + + + + Threshold for D-score PTM site location score. + MS + MS:1002557 + D-Score threshold + + + + + Threshold for D-score PTM site location score. + PSI:PI + + + + + + + + + + + + + + + Threshold for MD-score PTM site location score. + MS + MS:1002558 + MD-Score threshold + + + + + Threshold for MD-score PTM site location score. + PSI:PI + + + + + + + + + + + + + + + Threshold for H-score PTM site location score. + MS + MS:1002559 + H-Score threshold + + + + + Threshold for H-score PTM site location score. + PSI:PI + + + + + + + + + + + + + + + Threshold for DeBunker PTM site location score. + MS + MS:1002560 + DeBunker:score threshold + + + + + Threshold for DeBunker PTM site location score. + PSI:PI + + + + + + + + + + + + + + + Threshold for Mascot PTM site assignment confidence. + MS + MS:1002561 + Mascot:PTM site assignment confidence threshold + + + + + Threshold for Mascot PTM site assignment confidence. + PSI:PI + + + + + + + + + + + + + + + Threshold for MSQuant:PTM-score. + MS + MS:1002562 + MSQuant:PTM-score threshold + + + + + Threshold for MSQuant:PTM-score. + PSI:PI + + + + + + + + + + + + + + + Threshold for MaxQuant:PTM Score. + MS + MS:1002563 + MaxQuant:PTM Score threshold + + + + + Threshold for MaxQuant:PTM Score. + PSI:PI + + + + + + + + + + + + + + + Threshold for MaxQuant:P-site localization probability. + MS + MS:1002564 + MaxQuant:P-site localization probability threshold + + + + + Threshold for MaxQuant:P-site localization probability. + PSI:PI + + + + + + + + + + + + + + + Threshold for MaxQuant:PTM Delta Score. + MS + MS:1002565 + MaxQuant:PTM Delta Score threshold + + + + + Threshold for MaxQuant:PTM Delta Score. + PSI:PI + + + + + + + + + + + + + + + Threshold for MaxQuant:Phospho (STY) Probabilities. + MS + MS:1002566 + MaxQuant:Phospho (STY) Probabilities threshold + + + + + Threshold for MaxQuant:Phospho (STY) Probabilities. + PSI:PI + + + + + + + + + + + + + + + Threshold for phosphoRS score. + MS + MS:1002567 + phosphoRS score threshold + + + + + Threshold for phosphoRS score. + PSI:PI + + + + + + + + + + + + + + + Threshold for phosphoRS site probability. + MS + MS:1002568 + phosphoRS site probability threshold + + + + + Threshold for phosphoRS site probability. + PSI:PI + + + + + + + + + + + + + + + Number of spectra processed at once in a ProteomeDiscoverer search. + MS + MS:1002569 + ProteomeDiscoverer:Number of Spectra Processed At Once + + + + + Number of spectra processed at once in a ProteomeDiscoverer search. + PSI:PI + + + + + + + + + + + + + + + A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group. + MS + MS:1002570 + sequence multiply subsumable protein + + + + + A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group. + PSI:PI + + + + + + + + + + + + + + + A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group. + MS + MS:1002571 + spectrum multiply subsumable protein + + + + + A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group. + PSI:PI + + + + + + + + + Estimated statistical threshold used for protein detection. + MS + MS:1002572 + protein detection statistical threshold + + + + + Estimated statistical threshold used for protein detection. + PSI:MS + + + + + + + + + Estimated statistical threshold used for spectrum identification. + MS + MS:1002573 + spectrum identification statistical threshold + + + + + Estimated statistical threshold used for spectrum identification. + PSI:MS + + + + + + + + + A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. + MS + MS:1002574 + ASAPRatio + + + + + A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc. + PSI:PI + + + + + + + + + Tide open-source sequence search program developed at the University of Washington. + MS + MS:1002575 + Tide + + + + + Tide open-source sequence search program developed at the University of Washington. + PMID:21761931 + + + + + + + + + Andromeda result file output format. + MS + MS:1002576 + Andromeda result format + + + + + Andromeda result file output format. + PSI:PI + + + + + + + + + SCIEX 2000 QTRAP. + MS + MS:1002577 + 2000 QTRAP + + + + + SCIEX 2000 QTRAP. + PSI:MS + + + + + + + + + SCIEX 2500 QTRAP. + MS + MS:1002578 + 2500 QTRAP + + + + + SCIEX 2500 QTRAP. + PSI:MS + + + + + + + + + SCIEX 3500 QTRAP. + MS + MS:1002579 + 3500 QTRAP + + + + + SCIEX 3500 QTRAP. + PSI:MS + + + + + + + + + SCIEX QTRAP 4500. + MS + MS:1002580 + QTRAP 4500 + + + + + SCIEX QTRAP 4500. + PSI:MS + + + + + + + + + SCIEX QTRAP 6500. + MS + MS:1002581 + QTRAP 6500 + + + + + SCIEX QTRAP 6500. + PSI:MS + + + + + + + + + SCIEX QTRAP 6500+. + MS + MS:1002582 + QTRAP 6500+ + + + + + SCIEX QTRAP 6500+. + PSI:MS + + + + + + + + + SCIEX TripleTOF 4600 time-of-flight mass spectrometer. + MS + MS:1002583 + TripleTOF 4600 + + + + + SCIEX TripleTOF 4600 time-of-flight mass spectrometer. + PSI:MS + + + + + + + + + SCIEX TripleTOF 5600+ time-of-flight mass spectrometer. + MS + MS:1002584 + TripleTOF 5600+ + + + + + SCIEX TripleTOF 5600+ time-of-flight mass spectrometer. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 100 MS. + MS + MS:1002585 + API 100 + + + + + Applied Biosystems/MDS SCIEX API 100 MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 100LC MS. + MS + MS:1002586 + API 100LC + + + + + Applied Biosystems/MDS SCIEX API 100LC MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 165 MS. + MS + MS:1002587 + API 165 + + + + + Applied Biosystems/MDS SCIEX API 165 MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 300 MS. + MS + MS:1002588 + API 300 + + + + + Applied Biosystems/MDS SCIEX API 300 MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 350 MS. + MS + MS:1002589 + API 350 + + + + + Applied Biosystems/MDS SCIEX API 350 MS. + PSI:MS + + + + + + + + + Applied Biosystems/MDS SCIEX API 365 MS. + MS + MS:1002590 + API 365 + + + + + Applied Biosystems/MDS SCIEX API 365 MS. + PSI:MS + + + + + + + + + SCIEX Triple Quad 3500. + MS + MS:1002591 + Triple Quad 3500 + + + + + SCIEX Triple Quad 3500. + PSI:MS + + + + + + + + + SCIEX Triple Quad 4500. + MS + MS:1002592 + Triple Quad 4500 + + + + + SCIEX Triple Quad 4500. + PSI:MS + + + + + + + + + SCIEX Triple Quad 5500. + MS + MS:1002593 + Triple Quad 5500 + + + + + SCIEX Triple Quad 5500. + PSI:MS + + + + + + + + + SCIEX Triple Quad 6500. + MS + MS:1002594 + Triple Quad 6500 + + + + + SCIEX Triple Quad 6500. + PSI:MS + + + + + + + + + SCIEX Triple Quad 6500+. + MS + MS:1002595 + Triple Quad 6500+ + + + + + SCIEX Triple Quad 6500+. + PSI:MS + + + + + + + + + The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute. + MS + MS:1002596 + ProLuCID + + + + + The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute. + PMID:26171723 + + + + + + + + + MS1 file format for MS1 spectral data. + MS + MS:1002597 + MS1 format + + + + + MS1 file format for MS1 spectral data. + DOI:10.1002/rcm.1603 + PMID:15317041 + + + + + + + + + Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches. + MS + MS:1002598 + DTASelect + + + + + Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches. + PMID:12643522 + http://fields.scripps.edu/DTASelect/ + + + + + + + + + + + + + + + Spectral Hash key, an unique identifier for spectra. + MS + MS:1002599 + splash key + + + + + Spectral Hash key, an unique identifier for spectra. + PMID:27824832 + + + + + + + + + + Internal data and submission format of the PRIDE database. + MS + MS:1002600 + PRIDE XML + + + + + Internal data and submission format of the PRIDE database. + http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd + + + + + + + + + Tabular result format for proteomics and metabolomics experiments. + MS + MS:1002601 + mzTab + + + + + Tabular result format for proteomics and metabolomics experiments. + PMID:24980485 + http://www.psidev.info/mztab/ + + + + + + + + + + Reagent used in labeled quantification methods. + MS + MS:1002602 + sample label + + + + + Reagent used in labeled quantification methods. + PSI:PI + + + + + + + + + Isotope coded affinity tag reagent. + MS + MS:1002603 + ICAT reagent + + + + + Isotope coded affinity tag reagent. + PSI:PI + + + + + + + + + The name of the sample labelled with the heavy ICAT label. + MS + MS:1002604 + ICAT heavy reagent + + + + + The name of the sample labelled with the heavy ICAT label. + PSI:PI + + + + + + + + + The name of the sample labelled with the light ICAT label. + MS + MS:1002605 + ICAT light reagent + + + + + The name of the sample labelled with the light ICAT label. + PSI:PI + + + + + + + + + Isotope coded protein labeling reagent. + MS + MS:1002606 + ICPL reagent + + + + + Isotope coded protein labeling reagent. + PSI:PI + + + + + + + + + The name of the sample labelled with the ICPL reagent 0. + MS + MS:1002607 + ICPL reagent 0 + + + + + The name of the sample labelled with the ICPL reagent 0. + PSI:PI + + + + + + + + + The name of the sample labelled with the ICPL reagent 4. + MS + MS:1002608 + ICPL reagent 4 + + + + + The name of the sample labelled with the ICPL reagent 4. + PSI:PI + + + + + + + + + The name of the sample labelled with the ICPL reagent 6. + MS + MS:1002609 + ICPL reagent 6 + + + + + The name of the sample labelled with the ICPL reagent 6. + PSI:PI + + + + + + + + + The name of the sample labelled with the ICPL reagent 10. + MS + MS:1002610 + ICPL reagent 10 + + + + + The name of the sample labelled with the ICPL reagent 10. + PSI:PI + + + + + + + + + Stable isotope labeling with amino acids in cell culture reagent. + MS + MS:1002611 + SILAC reagent + + + + + Stable isotope labeling with amino acids in cell culture reagent. + PSI:PI + + + + + + + + + The name of the sample labelled with the heavy SILAC label. + MS + MS:1002612 + SILAC heavy reagent + + + + + The name of the sample labelled with the heavy SILAC label. + PSI:PI + + + + + + + + + The name of the sample labelled with the medium SILAC label. + MS + MS:1002613 + SILAC medium reagent + + + + + The name of the sample labelled with the medium SILAC label. + PSI:PI + + + + + + + + + The name of the sample labelled with the light SILAC label. + MS + MS:1002614 + SILAC light reagent + + + + + The name of the sample labelled with the light SILAC label. + PSI:PI + + + + + + + + + Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling. + MS + MS:1002615 + TMT reagent + + + + + Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 126. + MS + MS:1002616 + TMT reagent 126 + + + + + The name of the sample labelled with the TMT reagent 126. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 127. + MS + MS:1002617 + TMT reagent 127 + + + + + The name of the sample labelled with the TMT reagent 127. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 128. + MS + MS:1002618 + TMT reagent 128 + + + + + The name of the sample labelled with the TMT reagent 128. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 129. + MS + MS:1002619 + TMT reagent 129 + + + + + The name of the sample labelled with the TMT reagent 129. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 130. + MS + MS:1002620 + TMT reagent 130 + + + + + The name of the sample labelled with the TMT reagent 130. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 131. + MS + MS:1002621 + TMT reagent 131 + + + + + The name of the sample labelled with the TMT reagent 131. + PSI:PI + + + + + + + + + Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent. + MS + MS:1002622 + iTRAQ reagent + + + + + Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent. + PSI:PI + + + + + + + + + The name of the sample labelled with the iTRAQ reagent 113. + MS + MS:1002623 + iTRAQ reagent 113 + + + + + The name of the sample labelled with the iTRAQ reagent 113. + PSI:PI + + + + + + + + + The name of the sample labelled with the iTRAQ reagent 114. + MS + MS:1002624 + iTRAQ reagent 114 + + + + + The name of the sample labelled with the iTRAQ reagent 114. + PSI:PI + + + + + + + + + The name of the sample labelled with the iTRAQ reagent 115. + MS + MS:1002625 + iTRAQ reagent 115 + + + + + The name of the sample labelled with the iTRAQ reagent 115. + PSI:PI + + + + + + + + + The name of the sample labelled with the iTRAQ reagent 116. + MS + MS:1002626 + iTRAQ reagent 116 + + + + + The name of the sample labelled with the iTRAQ reagent 116. + PSI:PI + + + + + + + + + The name of the sample labelled with the iTRAQ reagent 117. + MS + MS:1002627 + iTRAQ reagent 117 + + + + + The name of the sample labelled with the iTRAQ reagent 117. + PSI:PI + + + + + + + + + The name of the sample labelled with the iTRAQ reagent 118. + MS + MS:1002628 + iTRAQ reagent 118 + + + + + The name of the sample labelled with the iTRAQ reagent 118. + PSI:PI + + + + + + + + + The name of the sample labelled with the iTRAQ reagent 119. + MS + MS:1002629 + iTRAQ reagent 119 + + + + + The name of the sample labelled with the iTRAQ reagent 119. + PSI:PI + + + + + + + + + The name of the sample labelled with the iTRAQ reagent 121. + MS + MS:1002630 + iTRAQ reagent 121 + + + + + The name of the sample labelled with the iTRAQ reagent 121. + PSI:PI + + + + + + + + + Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy). + EThcD + MS + MS:1002631 + electron-transfer/higher-energy collision dissociation + + + + + Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy). + PSI:PI + + + + + + + + + + + + + + + Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + MS + MS:1002632 + jPOST dataset identifier + + + + + Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + PSI:PI + + + + + + + + + + + + + + + URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + MS + MS:1002633 + jPOST dataset URI + + + + + URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + PSI:PI + + + + + + + + + Thermo Scientific Q Exactive Plus. + MS + MS:1002634 + Q Exactive Plus + + + + + Thermo Scientific Q Exactive Plus. + PSI:PI + + + + + + + + + Proteogenomics search performed. + MS + MS:1002635 + proteogenomics search + + + + + Proteogenomics search performed. + PSI:PI + + + + + + + + + Proteogenomics attribute. + MS + MS:1002636 + proteogenomics attribute + + + + + Proteogenomics attribute. + PSI:PI + + + + + + + + + + + + + + + The name or number of the chromosome to which a given peptide has been mapped. + MS + MS:1002637 + chromosome name + + + + + The name or number of the chromosome to which a given peptide has been mapped. + PSI:PI + + + + + + + + + + + + + + + The strand (+ or -) to which the peptide has been mapped. + MS + MS:1002638 + chromosome strand + + + + + The strand (+ or -) to which the peptide has been mapped. + PSI:PI + + + + + + + + + + + + + + + OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system. + MS + MS:1002639 + This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome. + peptide start on chromosome + true + + + + + OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system. + PSI:PI + + + + + + + + + + + + + + + The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system. + MS + MS:1002640 + peptide end on chromosome + + + + + The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system. + PSI:PI + + + + + + + + + + + + + + + The number of exons to which the peptide has been mapped. + MS + MS:1002641 + peptide exon count + + + + + The number of exons to which the peptide has been mapped. + PSI:PI + + + + + + + + + + + + + + + A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length. + MS + MS:1002642 + peptide exon nucleotide sizes + + + + + A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length. + PSI:PI + + + + + + + + + + + + + + + A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome. + MS + MS:1002643 + peptide start positions on chromosome + + + + + A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome. + PSI:PI + + + + + + + + + + + + + + + The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference. + MS + MS:1002644 + genome reference version + + + + + The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference. + PSI:PI + + + + + + + + + + Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data. + MS + MS:1002645 + MSDK + + + + + Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data. + PSI:PI + http://msdk.github.io/ + + + + + + + + + + + + + + Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated. + nativeID format, combined spectra + MS + MS:1002646 + native spectrum identifier format, combined spectra + + + + + Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated. + PSI:PI + + + + + + + + + + + + + + + Thermo comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002647 + Thermo nativeID format, combined spectra + + + + + Thermo comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Waters comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002648 + Waters nativeID format, combined spectra + + + + + Waters comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + WIFF comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002649 + WIFF nativeID format, combined spectra + + + + + WIFF comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002650 + Bruker/Agilent YEP nativeID format, combined spectra + + + + + Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002651 + Bruker BAF nativeID format, combined spectra + + + + + Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002652 + The nativeID must be the same as the source file ID. + Bruker FID nativeID format, combined spectra + + + + + Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002653 + Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. + multiple peak list nativeID format, combined spectra + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002654 + The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. + single peak list nativeID format, combined spectra + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002655 + Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. + scan number only nativeID format, combined spectra + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002656 + Used for conversion from mzData. The spectrum id attribute is referenced. + spectrum identifier nativeID format, combined spectra + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002657 + A unique identifier of a spectrum stored in an mzML file. + mzML unique identifier, combined spectra + + + + + Comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + Identification parameter for the search engine run. + MS + MS:1002658 + identification parameter + + + + + Identification parameter for the search engine run. + PSI:PI + + + + + + + + + Text-based format used by UniProtKB for sequence entries. + MS + MS:1002659 + UniProtKB text sequence format + + + + + Text-based format used by UniProtKB for sequence entries. + PSI:PI + + + + + + + + + XML-based format used by UniProtKB for sequence entries. + MS + MS:1002660 + UniProtKB XML sequence format + + + + + XML-based format used by UniProtKB for sequence entries. + PSI:PI + + + + + + + + + Morpheus search engine. + MS + MS:1002661 + Morpheus + + + + + Morpheus search engine. + PMID:23323968 + + + + + + + + + + + + + + + + + + + + + Morpheus score for PSMs. + MS + MS:1002662 + Morpheus:Morpheus score + + + + + Morpheus score for PSMs. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Summed Morpheus score for protein groups. + MS + MS:1002663 + Morpheus:summed Morpheus score + + + + + Summed Morpheus score for protein groups. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Parent term for interaction scores derived from cross-linking. + MS + MS:1002664 + interaction score derived from cross-linking + + + + + Parent term for interaction scores derived from cross-linking. + PSI:PI + + + + + + + + + ([0-9]+)[.]([a|b]):([0-9]+|null):([-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][+-][0-9]+)?):(true|false) + MS + MS:1002665 + regular expression for interaction scores derived from cross-linking + + + + + ([0-9]+)[.]([a|b]):([0-9]+|null):([-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][+-][0-9]+)?):(true|false) + PSI:PI + + + + + + + + + Bruker Daltonics' impact II. + MS + MS:1002666 + impact II + + + + + Bruker Daltonics' impact II. + PSI:MS + + + + + + + + + Bruker Daltonics' impact HD. + MS + MS:1002667 + impact HD + + + + + Bruker Daltonics' impact HD. + PSI:MS + + + + + + + + + + + + + + + Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114. + MS + MS:1002668 + frag: iTRAQ 4plex reporter ion + + + + + Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114. + PSI:PI + + + + + + + + + + + + + + + Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113. + MS + MS:1002669 + frag: iTRAQ 8plex reporter ion + + + + + Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113. + PSI:PI + + + + + + + + + + + + + + + Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N. + MS + MS:1002670 + frag: TMT reporter ion + + + + + Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N. + PSI:PI + + + + + + + + + + + + + + + Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C. + MS + MS:1002671 + frag: TMT ETD reporter ion + + + + + Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C. + PSI:PI + + + + + + + + + No statistical threshold for accepting or rejecting that a modification position. + MS + MS:1002672 + no modification threshold + + + + + No statistical threshold for accepting or rejecting that a modification position. + PSI:PI + + + + + + + + + Cross-Linking MS search engine. + MS + MS:1002673 + OpenXQuest + + + + + Cross-Linking MS search engine. + PSI:PI + + + + + + + + + SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer. + MS + MS:1002674 + X500R QTOF + + + + + SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer. + PSI:MS + + + + + + + + + + + + + + This subsection describes terms which can describe details of cross-linking results. + MS + MS:1002675 + cross-linking result details + + + + + This subsection describes terms which can describe details of cross-linking results. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + Estimation of the global false discovery rate of proteins-pairs in cross-linking experiments. + MS + MS:1002676 + protein-pair-level global FDR + + + + + Estimation of the global false discovery rate of proteins-pairs in cross-linking experiments. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + Estimation of the global false discovery rate of residue-pairs in cross-linking experiments. + MS + MS:1002677 + residue-pair-level global FDR + + + + + Estimation of the global false discovery rate of residue-pairs in cross-linking experiments. + PSI:PI + + + + + + + + + A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation. + MS + MS:1002678 + supplemental beam-type collision-induced dissociation + + + + + A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation. + PSI:MS + + + + + + + + + The dissociation of an ion after supplemental collisional excitation. + MS + MS:1002679 + supplemental collision-induced dissociation + + + + + The dissociation of an ion after supplemental collisional excitation. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion. + MS + MS:1002680 + supplemental collision energy + + + + + Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + OpenXQuest's combined score for a cross-link spectrum match. + MS + MS:1002681 + OpenXQuest:combined score + + + + + OpenXQuest's combined score for a cross-link spectrum match. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + OpenXQuest's cross-correlation of cross-linked ions subscore. + MS + MS:1002682 + OpenXQuest:xcorr xlink + + + + + OpenXQuest's cross-correlation of cross-linked ions subscore. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + OpenXQuest's cross-correlation of unlinked ions subscore. + MS + MS:1002683 + OpenXQuest:xcorr common + + + + + OpenXQuest's cross-correlation of unlinked ions subscore. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + OpenXQuest's match-odds subscore. + MS + MS:1002684 + OpenXQuest:match-odds + + + + + OpenXQuest's match-odds subscore. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + OpenXQuest's sum of matched peak intensity subscore. + MS + MS:1002685 + OpenXQuest:intsum + + + + + OpenXQuest's sum of matched peak intensity subscore. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + OpenXQuest's weighted percent of total ion current subscore. + MS + MS:1002686 + OpenXQuest:wTIC + + + + + OpenXQuest's weighted percent of total ion current subscore. + PSI:PI + + + + + + + + + Attribute of an item in the result of mass spectrometry proteomics data analysis. + MS + MS:1002687 + analysis attribute + + + + + Attribute of an item in the result of mass spectrometry proteomics data analysis. + PSI:PI + + + + + + + + + Statistic derived from a post-translational modification localization analysis. + MS + MS:1002688 + PTM localization attribute + + + + + Statistic derived from a post-translational modification localization analysis. + PSI:PI + + + + + + + + + Statistic for a single item derived from a post-translational modification localization analysis. + MS + MS:1002689 + PTM localization single result statistic + + + + + Statistic for a single item derived from a post-translational modification localization analysis. + PSI:PI + + + + + + + + + Statistic for all items derived from a post-translational modification localization analysis. + MS + MS:1002690 + PTM localization result list statistic + + + + + Statistic for all items derived from a post-translational modification localization analysis. + PSI:PI + + + + + + + + + Global false localization rate for all localizations in a dataset. + MS + MS:1002691 + global FLR + + + + + Global false localization rate for all localizations in a dataset. + PSI:PI + + + + + + + + + Local false localization rate for the bottom item in list of localizations sorted from most to least confident. + MS + MS:1002692 + local FLR at threshold + + + + + Local false localization rate for the bottom item in list of localizations sorted from most to least confident. + PSI:PI + + + + + + + + + Attribute of an identification item in the result of mass spectrometry proteomics data analysis. + MS + MS:1002693 + identification attribute + + + + + Attribute of an identification item in the result of mass spectrometry proteomics data analysis. + PSI:PI + + + + + + + + + Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis. + MS + MS:1002694 + single identification result attribute + + + + + Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis. + PSI:PI + + + + + + + + + Fragment ion corresponding to an isobaric label artifact. + MS + MS:1002695 + frag: isobaric label ion + + + + + Fragment ion corresponding to an isobaric label artifact. + PSI:PI + + + + + + + + + Fragment ion is an isotopic peak other than that monoisotopic peak. This is used in conjuction with another ion type, such as frag: y ion. + MS + MS:1002697 + secondary isotope peak + + + + + Fragment ion is an isotopic peak other than that monoisotopic peak. This is used in conjuction with another ion type, such as frag: y ion. + PSI:PI + + + + + + + + + An attribute of the protein cluster concept as used in mzIdentML. + MS + MS:1002698 + protein cluster identification attribute + + + + + An attribute of the protein cluster concept as used in mzIdentML. + PSI:PI + + + + + + + + + General property of an entire result list. + MS + MS:1002699 + result list attribute + + + + + General property of an entire result list. + PSI:PI + + + + + + + + + General property of the list of all PSMs. + MS + MS:1002700 + PSM-level result list attribute + + + + + General property of the list of all PSMs. + PSI:PI + + + + + + + + + Statistic pertaining to the full list of all PSMs. + MS + MS:1002701 + PSM-level result list statistic + + + + + Statistic pertaining to the full list of all PSMs. + PSI:PI + + + + + + + + + General property of all peptide sequences in the list. + MS + MS:1002702 + peptide sequence-level result list attribute + + + + + General property of all peptide sequences in the list. + PSI:PI + + + + + + + + + Statistic pertaining to all peptide sequences in the list. + MS + MS:1002703 + peptide sequence-level result list statistic + + + + + Statistic pertaining to all peptide sequences in the list. + PSI:PI + + + + + + + + + Attribute of an entire protein list. + MS + MS:1002704 + protein-level result list attribute + + + + + Attribute of an entire protein list. + PSI:PI + + + + + + + + + A statistical metric of an entire protein list. + MS + MS:1002705 + protein-level result list statistic + + + + + A statistical metric of an entire protein list. + PSI:PI + + + + + + + + + Attrbiute of an entire list of protein groups. + MS + MS:1002706 + protein group-level result list statistic + + + + + Attrbiute of an entire list of protein groups. + PSI:PI + + + + + + + + + Regular expression for LysargiNase. + MS + MS:1002707 + (?=[KR]) + + + + + Regular expression for LysargiNase. + PSI:PI + + + + + + + + + + + + + + + Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues. + Tryp-N + MS + MS:1002708 + LysargiNase + + + + + Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues. + PMID:25419962 + + + + + + + + A data type representing more than a single value. + MS + MS:1002709 + compound data type + + + + + + + + + A data type defining a list of values of a single type. + MS + MS:1002710 + list of type + + + + + + + + + + + + + + + A list of xsd:string. + MS + MS:1002711 + list of strings + + + + + + + + + + + + + + + A list of xsd:integer. + MS + MS:1002712 + list of integers + + + + + + + + + + + + + + + A list of xsd:float. + MS + MS:1002713 + list of floats + + + + + + + + + LECO bench-top GC time-of-flight mass spectrometer. + MS + MS:1002719 + Pegasus BT + + + + + LECO bench-top GC time-of-flight mass spectrometer. + PSI:PI + + + + + + + + + PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra. + MS + MS:1002720 + MSPathFinder + + + + + PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + MSPathFinder spectral E-value. + MS + MS:1002721 + MSPathFinder:SpecEValue + + + + + MSPathFinder spectral E-value. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + MSPathFinder E-value. + MS + MS:1002722 + MSPathFinder:EValue + + + + + MSPathFinder E-value. + PSI:PI + + + + + + + + + + + + + + + + MSPathFinder Q-value. + MS + MS:1002723 + MSPathFinder:QValue + + + + + MSPathFinder Q-value. + PSI:PI + + + + + + + + + + + + + + + MSPathFinder peptide-level Q-value. + MS + MS:1002724 + MSPathFinder:PepQValue + + + + + MSPathFinder peptide-level Q-value. + PSI:PI + + + + + + + + + + + + + + + MSPathFinder raw score. + MS + MS:1002725 + MSPathFinder:RawScore + + + + + MSPathFinder raw score. + PSI:PI + + + + + + + + + Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. + MS + MS:1002726 + SYNAPT G2-Si + + + + + Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. + PSI:PI + + + + + + + + + Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. + MS + MS:1002727 + MALDI SYNAPT G2-Si + + + + + Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer. + PSI:PI + + + + + + + + + Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer. + MS + MS:1002728 + Vion IMS QTof + + + + + Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer. + PSI:PI + + + + + + + + + Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer. + MS + MS:1002729 + Xevo G2-XS Tof + + + + + Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer. + PSI:PI + + + + + + + + + Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer. + MS + MS:1002730 + Xevo TQ-XS + + + + + Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer. + PSI:PI + + + + + + + + + Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer. + MS + MS:1002731 + Xevo TQ-S micro + + + + + Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer. + PSI:PI + + + + + + + + + Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. + MS + MS:1002732 + Orbitrap Fusion Lumos + + + + + Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. + PSI:PI + + + + + + + + + + + + + + + The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting. + MS + MS:1002733 + peptide-level spectral count + + + + + The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting. + PSI:PI + + + + + + + + + + + + + + + The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting. + MS + MS:1002734 + peptide ion-level spectral count + + + + + The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting. + PSI:PI + + + + + + + + + The data type of the value reported in a QuantLayer for a feature. + MS + MS:1002735 + feature-level quantification datatype + + + + + The data type of the value reported in a QuantLayer for a feature. + PSI:PI + + + + + + + + + The data type of the value reported in a QuantLayer for a PSM. + MS + MS:1002736 + PSM-level quantification datatype + + + + + The data type of the value reported in a QuantLayer for a PSM. + PSI:PI + + + + + + + + + The data type of the value reported in a QuantLayer for a peptide. + MS + MS:1002737 + peptide-level quantification datatype + + + + + The data type of the value reported in a QuantLayer for a peptide. + PSI:PI + + + + + + + + + The data type of the value reported in a QuantLayer for a protein. + MS + MS:1002738 + protein-level quantification datatype + + + + + The data type of the value reported in a QuantLayer for a protein. + PSI:PI + + + + + + + + + The data type of the value reported in a QuantLayer for a protein group. + MS + MS:1002739 + protein group-level quantification datatype + + + + + The data type of the value reported in a QuantLayer for a protein group. + PSI:PI + + + + + + + + + Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location. + MS + MS:1002740 + unmapped peptide + + + + + Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location. + PSI:PI + + + + + + + + + Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location. + MS + MS:1002741 + unmapped protein + + + + + Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location. + PSI:PI + + + + + + + + + A data array of noise values. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1002742 + noise array + + + + + A data array of noise values. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + + + + + + + A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array). + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1002743 + sampled noise m/z array + + + + + A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array). + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + + + + + + + A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array). + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1002744 + sampled noise intensity array + + + + + A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array). + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array). + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1002745 + sampled noise baseline array + + + + + A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array). + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + Compression using MS-Numpress linear prediction compression and zlib. + MS + MS:1002746 + MS-Numpress linear prediction compression followed by zlib compression + + + + + Compression using MS-Numpress linear prediction compression and zlib. + https://github.com/ms-numpress/ms-numpress + + + + + + + + + Compression using MS-Numpress positive integer compression and zlib. + MS + MS:1002747 + MS-Numpress positive integer compression followed by zlib compression + + + + + Compression using MS-Numpress positive integer compression and zlib. + https://github.com/ms-numpress/ms-numpress + + + + + + + + + Compression using MS-Numpress short logged float compression and zlib. + MS + MS:1002748 + MS-Numpress short logged float compression followed by zlib compression + + + + + Compression using MS-Numpress short logged float compression and zlib. + https://github.com/ms-numpress/ms-numpress + + + + + + + + + + + + + + + Means that Mascot has integrated the search results of database and spectral library search into a single data set. + MS + MS:1002749 + Mascot:IntegratedSpectralLibrarySearch + + + + + Means that Mascot has integrated the search results of database and spectral library search into a single data set. + PSI:PI + + + + + + + + + Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches. + MS + MS:1002750 + NIST MSPepSearch + + + + + Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches. + PSI:PI + + + + + + + + + MSP text format defined by the NIST. + MS + MS:1002751 + NIST MSP format + + + + + MSP text format defined by the NIST. + PSI:PI + + + + + + + + + Database containing spectra. + MS + MS:1002752 + database type spectral library + + + + + Database containing spectra. + PSI:PI + + + + + + + + + Value range for scores. + MS + MS:1002753 + value between 0 and 1000 inclusive + + + + + Value range for scores. + PSI:PI + + + + + + + + + + + + + + + + + + + + + MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum. + MS + MS:1002754 + MSPepSearch:score + + + + + MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum. + PSI:PI + + + + + + + + + A combined MS2 (with fragment ions) and spectral library search. + MS + MS:1002755 + combined ms-ms + spectral library search + + + + + A combined MS2 (with fragment ions) and spectral library search. + PSI:PI + + + + + + + + + Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow. + MS + MS:1002756 + iodoTMT quantitation analysis + + + + + Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow. + PMID:24926564 + PSI:PI + + + + + + + + + Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow. + MS + MS:1002757 + glyco-TMT quantitation analysis + + + + + Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow. + PMID:22455665 + PSI:PI + + + + + + + + + Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow. + MS + MS:1002758 + aminoxyTMT quantitation analysis + + + + + Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow. + PMID:25337643 + PSI:PI + + + + + + + + + Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow. + MS + MS:1002759 + hydrazideTMT quantitation analysis + + + + + Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow. + PMID:25337643 + PSI:PI + + + + + + + + + Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow. + MS + MS:1002760 + iTRAQH quantitation analysis + + + + + Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow. + PMID:22926130 + PSI:PI + + + + + + + + + Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow. + MS + MS:1002761 + DiART quantitation analysis + + + + + Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow. + PMID:20715779 + PSI:PI + + + + + + + + + Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow. + MS + MS:1002762 + DiLeu quantitation analysis + + + + + Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow. + PMID:20715779 + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 127N. + MS + MS:1002763 + TMT reagent 127N + + + + + The name of the sample labelled with the TMT reagent 127N. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 127C. + MS + MS:1002764 + TMT reagent 127C + + + + + The name of the sample labelled with the TMT reagent 127C. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 128N. + MS + MS:1002765 + TMT reagent 128N + + + + + The name of the sample labelled with the TMT reagent 128N. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 128C. + MS + MS:1002766 + TMT reagent 128C + + + + + The name of the sample labelled with the TMT reagent 128C. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 129N. + MS + MS:1002767 + TMT reagent 129N + + + + + The name of the sample labelled with the TMT reagent 129N. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 129C. + MS + MS:1002768 + TMT reagent 129C + + + + + The name of the sample labelled with the TMT reagent 129C. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 130N. + MS + MS:1002769 + TMT reagent 130N + + + + + The name of the sample labelled with the TMT reagent 130N. + PSI:PI + + + + + + + + + The name of the sample labelled with the TMT reagent 130C. + MS + MS:1002770 + TMT reagent 130C + + + + + The name of the sample labelled with the TMT reagent 130C. + PSI:PI + + + + + + + + + Deuterium isobaric amine reactive tag labeling reagent. + MS + MS:1002771 + DiART reagent + + + + + Deuterium isobaric amine reactive tag labeling reagent. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiART reagent 114. + MS + MS:1002772 + DiART reagent 114 + + + + + The name of the sample labelled with the DiART reagent 114. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiART reagent 115. + MS + MS:1002773 + DiART reagent 115 + + + + + The name of the sample labelled with the DiART reagent 115. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiART reagent 116. + MS + MS:1002774 + DiART reagent 116 + + + + + The name of the sample labelled with the DiART reagent 116. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiART reagent 117. + MS + MS:1002775 + DiART reagent 117 + + + + + The name of the sample labelled with the DiART reagent 117. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiART reagent 118. + MS + MS:1002776 + DiART reagent 118 + + + + + The name of the sample labelled with the DiART reagent 118. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiART reagent 119. + MS + MS:1002777 + DiART reagent 119 + + + + + The name of the sample labelled with the DiART reagent 119. + PSI:PI + + + + + + + + + Dimethyl leucine labeling reagent. + MS + MS:1002778 + DiLeu reagent + + + + + Dimethyl leucine labeling reagent. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiLeu reagent 115. + MS + MS:1002779 + DiLeu reagent 115 + + + + + The name of the sample labelled with the DiLeu reagent 115. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiLeu reagent 116. + MS + MS:1002780 + DiLeu reagent 116 + + + + + The name of the sample labelled with the DiLeu reagent 116. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiLeu reagent 117. + MS + MS:1002781 + DiLeu reagent 117 + + + + + The name of the sample labelled with the DiLeu reagent 117. + PSI:PI + + + + + + + + + The name of the sample labelled with the DiLeu reagent 118. + MS + MS:1002782 + DiLeu reagent 118 + + + + + The name of the sample labelled with the DiLeu reagent 118. + PSI:PI + + + + + + + + + The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002783 + 6550 iFunnel Q-TOF LC/MS + + + + + The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002784 + 6550A iFunnel Q-TOF LC/MS + + + + + The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002785 + 6520B Q-TOF LC/MS + + + + + The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002786 + 6530A Q-TOF LC/MS + + + + + The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002787 + 6530B Q-TOF LC/MS + + + + + The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002788 + 6538 Q-TOF LC/MS + + + + + The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002789 + 6540 Q-TOF LC/MS + + + + + The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002790 + 6542 Q-TOF LC/MS + + + + + The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002791 + 6545 Q-TOF LC/MS + + + + + The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002792 + 6560 Q-TOF LC/MS + + + + + The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002793 + 6570 Q-TOF LC/MS + + + + + The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. + MS + MS:1002794 + 6120B Quadrupole LC/MS + + + + + The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. + PSI:MS + + + + + + + + + The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. + MS + MS:1002795 + 6150 Quadrupole LC/MS + + + + + The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. + PSI:MS + + + + + + + + + The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002796 + 6224 Time-of-Flight LC/MS + + + + + The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002797 + 6230A Time-of-Flight LC/MS + + + + + The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + MS + MS:1002798 + 6230B Time-of-Flight LC/MS + + + + + The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. + PSI:MS + + + + + + + + + The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1002799 + 6430 Triple Quadrupole LC/MS + + + + + The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1002800 + 6495A Triple Quadrupole LC/MS + + + + + The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1002801 + 6495B Triple Quadrupole LC/MS + + + + + The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1002802 + 7000A Triple Quadrupole GC/MS + + + + + The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + MS + MS:1002803 + 7000B Triple Quadrupole GC/MS + + + + + The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. + MS + MS:1002804 + 7800 Quadrupole ICP-MS + + + + + The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. + PSI:MS + + + + + + + + + The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. + MS + MS:1002805 + 8800 Triple Quadrupole ICP-MS + + + + + The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer. + PSI:MS + + + + + + + + + Molecular entity having a net positive or negative electric charge. + MS + MS:1002806 + ion + + + + + Molecular entity having a net positive or negative electric charge. + PSI:MS + + + + + + + + + Adduct ion with positive ionization. + MS + MS:1002807 + positive mode adduct ion + + + + + Adduct ion with positive ionization. + PSI:MS + + + + + + + + + Adduct ion with negative ionization. + MS + MS:1002808 + negative mode adduct ion + + + + + Adduct ion with negative ionization. + PSI:MS + + + + + + + + + + + + + + Nonphysical characteristic attributed to an adduct ion. + MS + MS:1002809 + adduct ion attribute + + + + + Nonphysical characteristic attributed to an adduct ion. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator. + MS + MS:1002810 + adduct ion X m/z + + + + + Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator. + PSI:MS + + + + + + + + + + + + + + + Isotope of the matrix molecule M of an adduct formation. + MS + MS:1002811 + adduct ion isotope + + + + + Isotope of the matrix molecule M of an adduct formation. + PSI:MS + + + + + + + + + ([[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}][:digit:]{0,1}[+-]). + MS + MS:1002812 + Regular expression for adduct ion formula + + + + + ([[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}][:digit:]{0,1}[+-]). + PSI:PI + + + + + + + + + + + + + + + + + + + + + Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression. + MS + MS:1002813 + adduct ion formula + + + + + Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression. + PSI:MS + + + + + + + + + An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]. + Vs/cm^2 + MS + MS:1002814 + volt-second per square centimeter + + + + + An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated. + MS + MS:1002815 + inverse reduced ion mobility + + + + + Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1002816 + mean ion mobility array + + + + + Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + Bruker TDF raw file format. + MS + MS:1002817 + Bruker TDF format + + + + + Bruker TDF raw file format. + PSI:MS + + + + + + + + + Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. + MS + MS:1002818 + Bruker TDF nativeID format + + + + + Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + + + + + + + Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1002819 + Bruker TDF nativeID format, combined spectra + + + + + Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton. + M + 1.007276 + MS + MS:1002820 + M+H ion + + + + + Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton. + PSI:MS + + + + + + + + + Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M. + M - 1.007276 + MS + MS:1002821 + M-H ion + + + + + Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M. + PSI:MS + + + + + + + + + File format developed by the OpenMS team. + MS + MS:1002822 + OpenMS file format + + + + + File format developed by the OpenMS team. + PMID:27575624 + + + + + + + + + OpenMS intermediate identification format. + MS + MS:1002823 + idXML + + + + + OpenMS intermediate identification format. + PSI:PI + + + + + + + + + OpenMS feature file format. + MS + MS:1002824 + featureXML + + + + + OpenMS feature file format. + PSI:PI + + + + + + + + + OpenMS consensus map format. + MS + MS:1002825 + consensusXML + + + + + OpenMS consensus map format. + PSI:PI + + + + + + + + + MetaMorpheus search engine. + MS + MS:1002826 + MetaMorpheus + + + + + MetaMorpheus search engine. + https://github.com/smith-chem-wisc/MetaMorpheus + + + + + + + + + + + + + + + + + + + + + MetaMorpheus score for PSMs. + MS + MS:1002827 + MetaMorpheus:score + + + + + MetaMorpheus score for PSMs. + PSI:PI + + + + + + + + + + + + + + + + + + + + + MetaMorpheus score for protein groups. + MS + MS:1002828 + MetaMorpheus:protein score + + + + + MetaMorpheus score for protein groups. + PSI:PI + + + + + + + + + + + + + + + Feature intensity produced by XCMS findPeaks() from integrated peak intensity. + MS + MS:1002829 + XCMS:into + + + + + Feature intensity produced by XCMS findPeaks() from integrated peak intensity. + PSI:PI + + + + + + + + + + + + + + + Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity. + MS + MS:1002830 + XCMS:intf + + + + + Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity. + PSI:PI + + + + + + + + + + + + + + + Feature intensity produced by XCMS findPeaks() from maximum peak intensity. + MS + MS:1002831 + XCMS:maxo + + + + + Feature intensity produced by XCMS findPeaks() from maximum peak intensity. + PSI:PI + + + + + + + + + + + + + + + Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate. + MS + MS:1002832 + XCMS:area + + + + + Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate. + PSI:PI + + + + + + + + + Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired. + MS + MS:1002833 + alternating polarity mode + + + + + Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired. + PSI:PI + + + + + + + + + + + + + + + The Delta Score reported by Proteome Discoverer version 2. + MS + MS:1002834 + ProteomeDiscoverer:Delta Score + + + + + The Delta Score reported by Proteome Discoverer version 2. + PSI:PI + + + + + + + + + Thermo Fisher Scientific LTQ Orbitrap Classic. + MS + MS:1002835 + LTQ Orbitrap Classic + + + + + Thermo Fisher Scientific LTQ Orbitrap Classic. + PSI:MS + + + + + + + + + + + + + + + Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + MS + MS:1002836 + iProX dataset identifier + + + + + Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + PSI:PI + + + + + + + + + + + + + + + URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + MS + MS:1002837 + iProX dataset URI + + + + + URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + PSI:PI + + + + + + + + + mzMLb file format, mzML encapsulated within HDF5. + MS + MS:1002838 + mzMLb format + + + + + mzMLb file format, mzML encapsulated within HDF5. + PSI:PI + https://github.com/biospi/mzmlb + + + + + + + + + Conversion of a file format to Proteomics Standards Initiative mzMLb file format. + MS + MS:1002839 + Conversion to mzMLb + + + + + Conversion of a file format to Proteomics Standards Initiative mzMLb file format. + PSI:PI + + + + + + + + + + + + + + Data belonging to an external reference. + MS + MS:1002840 + external reference data + + + + + Data belonging to an external reference. + PSI:MS + + + + + + + + + + + + + + + The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray. + MS + MS:1002841 + external HDF5 dataset + + + + + The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The position in the external data where the array begins. + MS + MS:1002842 + external offset + + + + + The position in the external data where the array begins. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Describes how many fields an array contains. + MS + MS:1002843 + external array length + + + + + Describes how many fields an array contains. + PSI:PI + + + + + + + + + Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam. + MS + MS:1002844 + Experiment additional parameter + + + + + Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam. + PSI:PI + + + + + + + + + + + + + + + URI of one external file associated to the PRIDE experiment (maybe through a PX submission). + MS + MS:1002845 + Associated file URI + + + + + URI of one external file associated to the PRIDE experiment (maybe through a PX submission). + PSI:PI + + + + + + + + + + + + + + + URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). + MS + MS:1002846 + Associated raw file URI + + + + + URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). + PSI:PI + + + + + + + + + + + + + + + URI associated to one PX submission in ProteomeCentral. + MS + MS:1002847 + ProteomeCentral dataset URI + + + + + URI associated to one PX submission in ProteomeCentral. + PSI:PI + + + + + + + + + + + + + + + URI of one file labeled as 'Result', associated to one PX submission. + MS + MS:1002848 + Result file URI + + + + + URI of one file labeled as 'Result', associated to one PX submission. + PSI:PI + + + + + + + + + + + + + + + URI of one search engine output file associated to one PX submission. + MS + MS:1002849 + Search engine output file URI + + + + + URI of one search engine output file associated to one PX submission. + PSI:PI + + + + + + + + + + + + + + + URI of one of one search engine output file associated to one PX submission. + MS + MS:1002850 + Peak list file URI + + + + + URI of one of one search engine output file associated to one PX submission. + PSI:PI + + + + + + + + + + + + + + + URI of one file labeled as 'Other', associated to one PX submission. + MS + MS:1002851 + Other type file URI + + + + + URI of one file labeled as 'Other', associated to one PX submission. + PSI:PI + + + + + + + + + + + + + + + FTP location of one entire PX data set. + MS + MS:1002852 + Dataset FTP location + + + + + FTP location of one entire PX data set. + PSI:PI + + + + + + + + + A dataset which does not have an associated published manuscript. + MS + MS:1002853 + Dataset with no associated published manuscript + + + + + A dataset which does not have an associated published manuscript. + PSI:PI + + + + + + + + + Dataset has been peer-reviewed somehow. + MS + MS:1002854 + Peer-reviewed dataset + + + + + Dataset has been peer-reviewed somehow. + PSI:PI + + + + + + + + + Dataset that has not been peer-reviewed by any means. + MS + MS:1002855 + Non peer-reviewed dataset + + + + + Dataset that has not been peer-reviewed by any means. + PSI:PI + + + + + + + + + Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission. + MS + MS:1002856 + Supported dataset by repository + + + + + Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission. + PSI:PI + + + + + + + + + Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission. + MS + MS:1002857 + Unsupported dataset by repository + + + + + Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission. + PSI:PI + + + + + + + + + A dataset which has an associated manuscript pending for publication. + MS + MS:1002858 + Dataset with its publication pending + + + + + A dataset which has an associated manuscript pending for publication. + PSI:PI + + + + + + + + + + + + + + + Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE. + MS + MS:1002859 + Additional associated raw file URI + + + + + Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE. + PSI:PI + + + + + + + + + + + + + + + URI of one gel image file associated to one PX submission. + MS + MS:1002860 + Gel image file URI + + + + + URI of one gel image file associated to one PX submission. + PSI:PI + + + + + + + + + + + + + + + All the raw files included in the original dataset (or group of original datasets) have been reanalysed. + MS + MS:1002861 + Reprocessed complete dataset + + + + + All the raw files included in the original dataset (or group of original datasets) have been reanalysed. + PSI:PI + + + + + + + + + + + + + + + A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed. + MS + MS:1002862 + Reprocessed subset dataset + + + + + A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed. + PSI:PI + + + + + + + + + One dataset is a reanalysis of previously published data. + MS + MS:1002863 + Data derived from previous dataset + + + + + One dataset is a reanalysis of previously published data. + PSI:PI + + + + + + + + + No post-translational-modifications are been included in the identified peptides of one dataset. + MS + MS:1002864 + No PTMs are included in the dataset + + + + + No post-translational-modifications are been included in the identified peptides of one dataset. + PSI:PI + + + + + + + + + A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet. + MS + MS:1002865 + Accepted manuscript + + + + + A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet. + PSI:PI + + + + + + + + + + + + + + + Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet. + MS + MS:1002866 + Reference + + + + + Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet. + PSI:PI + + + + + + + + + This means that the experimental information available has been improved, for instance precursor charges were added. + MS + MS:1002867 + Experimental information has been refined since this experiment was originally made publicly available + + + + + This means that the experimental information available has been improved, for instance precursor charges were added. + PSI:PI + + + + + + + + + One dataset is not a reanalysis of previously published data. + MS + MS:1002868 + Original data + + + + + One dataset is not a reanalysis of previously published data. + PSI:PI + + + + + + + + + + Bioconductor package mzR for reading and writing mass spectrometry data files. + MS + MS:1002869 + mzR + + + + + Bioconductor package mzR for reading and writing mass spectrometry data files. + PSI:PI + + + + + + + + + + Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. + MS + MS:1002870 + MSnbase + + + + + Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. + PMID:22113085 + + + + + + + + + + Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments. + MS + MS:1002871 + CAMERA + + + + + Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments. + PMID:22111785 + + + + + + + + + + + + + + + Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + MS + MS:1002872 + Panorama Public dataset identifier + + + + + Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + PSI:PI + + + + + + + + + + + + + + + URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + MS + MS:1002873 + Panorama Public dataset URI + + + + + URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication. + PSI:PI + + + + + + + + + Thermo Scientific TSQ Altis Triple Quadrupole MS. + MS + MS:1002874 + TSQ Altis + + + + + Thermo Scientific TSQ Altis Triple Quadrupole MS. + PSI:PI + + + + + + + + + Thermo Scientific TSQ Quantis Triple Quadrupole MS. + MS + MS:1002875 + TSQ Quantis + + + + + Thermo Scientific TSQ Quantis Triple Quadrupole MS. + PSI:PI + + + + + + + + + Thermo Scientific TSQ 9000 Triple Quadrupole MS. + MS + MS:1002876 + TSQ 9000 + + + + + Thermo Scientific TSQ 9000 Triple Quadrupole MS. + PSI:PI + + + + + + + + + Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS. + MS + MS:1002877 + Q Exactive HF-X + + + + + Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS. + PSI:PI + + + + + + + + + Software for the analysis of small molecules. + MS + MS:1002878 + small molecule analysis software + + + + + Software for the analysis of small molecules. + PSI:PI + + + + + + + + + Metabolomics analysis software for LC-MS data from Nonlinear Dynamics. + MS + MS:1002879 + Progenesis QI + + + + + Metabolomics analysis software for LC-MS data from Nonlinear Dynamics. + PSI:PI + + + + + + + + + Metabolomics analysis software from Thermo Fisher Scientific. + MS + MS:1002880 + Compound Discoverer + + + + + Metabolomics analysis software from Thermo Fisher Scientific. + PSI:PI + + + + + + + + + Metabolite identification tool MyCompoundID. + MS + MS:1002881 + MyCompoundID + + + + + Metabolite identification tool MyCompoundID. + PMID:23373753 + PSI:PI + + + + + + + + + Function used to calculate the study variable quantification value. + MS + MS:1002882 + study variable average function + + + + + Function used to calculate the study variable quantification value. + PSI:PI + + + + + + + + + Median function. + MS + MS:1002883 + median + + + + + Median function. + PSI:PI + + + + + + + + + Function used to calculate the study variable quantification variation value. + MS + MS:1002884 + study variable variation function + + + + + Function used to calculate the study variable quantification variation value. + PSI:PI + + + + + + + + + Standard error function. + MS + MS:1002885 + standard error + + + + + Standard error function. + PSI:PI + + + + + + + + + The value reported in a small molecule quantification. + MS + MS:1002886 + small molecule quantification datatype + + + + + The value reported in a small molecule quantification. + PSI:PI + + + + + + + + + + + + + + + The normalised abundance produced by Progenesis QI LC-MS. + MS + MS:1002887 + Progenesis QI normalised abundance + + + + + The normalised abundance produced by Progenesis QI LC-MS. + PSI:PI + + + + + + + + + The confidence score produced by a small molecule analysis software. + MS + MS:1002888 + small molecule confidence measure + + + + + The confidence score produced by a small molecule analysis software. + PSI:PI + + + + + + + + + + + + + + + The confidence score produced by Progenesis QI. + MS + MS:1002889 + Progenesis MetaScope score + + + + + The confidence score produced by Progenesis QI. + PSI:PI + + + + + + + + + + + + + + + The fragmentation confidence score. + MS + MS:1002890 + fragmentation score + + + + + The fragmentation confidence score. + PSI:PI + + + + + + + + + + + + + + + The isotopic fit confidence score. + MS + MS:1002891 + isotopic fit score + + + + + The isotopic fit confidence score. + PSI:PI + + + + + + + + + + An attribute describing ion mobility searches. + MS + MS:1002892 + ion mobility attribute + + + + + An attribute describing ion mobility searches. + PSI:PI + + + + + + + + + Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided. + MS + MS:1002893 + ion mobility array + + + + + Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided. + PSI:PI + + + + + + + + + + + + + + + Unique chemical structure identifier for chemical compounds. + MS + MS:1002894 + InChIKey + + + + + Unique chemical structure identifier for chemical compounds. + PMID:273343401 + + + + + + + + + Compound identification information. + MS + MS:1002895 + small molecule identification attribute + + + + + Compound identification information. + PSI:PI + + + + + + + + + + + + + + + Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'. + MS + MS:1002896 + compound identification confidence level + + + + + Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'. + PMID:29748461 + + + + + + + + + + + + + + + OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'. + MS + MS:1002897 + This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. + isotopomer peak + true + + + + + OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'. + PSI:PI + + + + + + + + + Native format defined by scan=xsd:nonNegativeInteger. + MS + MS:1002898 + Shimadzu Biotech QTOF nativeID format + + + + + Native format defined by scan=xsd:nonNegativeInteger. + PSI:PI + + + + + + + + + msalign file format. + MS + MS:1002899 + msalign format + + + + + msalign file format. + PSI:MS + + + + + + + + + TopFD feature file format. + MS + MS:1002900 + feature format + + + + + TopFD feature file format. + PSI:MS + + + + + + + + + TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. + MS + MS:1002901 + TopPIC + + + + + TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. + PMID:27423895 + http://proteomics.informatics.iupui.edu/software/toppic/index.html + + + + + + + + + Top-down mass spectral feature detection. + MS + MS:1002902 + TopFD + + + + + Top-down mass spectral feature detection. + http://proteomics.informatics.iupui.edu/software/toppic/index.html + + + + + + + + + A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. + MS + MS:1002903 + TopMG + + + + + A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. + PMID:28453668 + http://proteomics.informatics.iupui.edu/software/topmg/index.html + + + + + + + + + Proteoform level information. + MS + MS:1002904 + proteoform-level identification attribute + + + + + Proteoform level information. + PSI:PI + + + + + + + + + Identification confidence metric for a proteoform. + MS + MS:1002905 + proteoform-level identification statistic + + + + + Identification confidence metric for a proteoform. + PSI:PI + + + + + + + + + Search engine specific proteoform scores. + MS + MS:1002906 + search engine specific score for proteoforms + + + + + Search engine specific proteoform scores. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the global false discovery rate of proteoforms. + MS + MS:1002907 + proteoform-level global FDR + + + + + Estimation of the global false discovery rate of proteoforms. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Estimation of the local false discovery rate of proteoforms. + MS + MS:1002908 + proteoform-level local FDR + + + + + Estimation of the local false discovery rate of proteoforms. + PSI:PI + + + + + + + + + Estimated statistical threshold at proteoform-level. + MS + MS:1002909 + proteoform-level statistical threshold + + + + + Estimated statistical threshold at proteoform-level. + PSI:PI + + + + + + + + + + + + + + + Threshold for the global false discovery rate of proteoforms. + MS + MS:1002910 + proteoform-level global FDR threshold + + + + + Threshold for the global false discovery rate of proteoforms. + PSI:PI + + + + + + + + + + + + + + + Threshold for the local false discovery rate of proteoforms. + MS + MS:1002911 + proteoform-level local FDR threshold + + + + + Threshold for the local false discovery rate of proteoforms. + PSI:PI + + + + + + + + + Search engine input parameters specific to TopPIC. + MS + MS:1002912 + TopPIC input parameter + + + + + Search engine input parameters specific to TopPIC. + PSI:PI + + + + + + + + + Fixed modifications for TopPIC searching. + MS + MS:1002913 + TopPIC:fixed modification + + + + + Fixed modifications for TopPIC searching. + PSI:PI + + + + + + + + + N-terminal forms of proteins allowed in TopPIC searching. + MS + MS:1002914 + TopPIC:N-term form + + + + + N-terminal forms of proteins allowed in TopPIC searching. + PSI:PI + + + + + + + + + + + + + + + Error tolerance for precursor and fragment masses in PPM. + MS + MS:1002915 + TopPIC:error tolerance + + + + + Error tolerance for precursor and fragment masses in PPM. + PSI:PI + + + + + + + + + + + + + + + Maximum value of the mass shift (in Dalton) of an unexpected modification. + MS + MS:1002916 + TopPIC:max shift + + + + + Maximum value of the mass shift (in Dalton) of an unexpected modification. + PSI:PI + + + + + + + + + + + + + + + Minimum value of the mass shift (in Dalton) of an unexpected modification. + MS + MS:1002917 + TopPIC:min shift + + + + + Minimum value of the mass shift (in Dalton) of an unexpected modification. + PSI:PI + + + + + + + + + + + + + + + Maximum number of unexpected modifications in a proteoform spectrum match. + MS + MS:1002918 + TopPIC:shift num + + + + + Maximum number of unexpected modifications in a proteoform spectrum match. + PSI:PI + + + + + + + + + + + + + + + Spectrum-level cutoff type for filtering identified proteoform spectrum matches. + MS + MS:1002919 + TopPIC:spectral cutoff type + + + + + Spectrum-level cutoff type for filtering identified proteoform spectrum matches. + PSI:PI + + + + + + + + + + + + + + + Spectrum-level cutoff value for filtering identified proteoform spectrum matches. + MS + MS:1002920 + TopPIC:spectral cutoff value + + + + + Spectrum-level cutoff value for filtering identified proteoform spectrum matches. + PSI:PI + + + + + + + + + + + + + + + Proteoform-level cutoff type for filtering identified proteoform spectrum matches. + MS + MS:1002921 + TopPIC:proteoform-level cutoff type + + + + + Proteoform-level cutoff type for filtering identified proteoform spectrum matches. + PSI:PI + + + + + + + + + + + + + + + Proteoform-level cutoff value for filtering identified proteoform spectrum matches. + MS + MS:1002922 + TopPIC:proteoform-level cutoff value + + + + + Proteoform-level cutoff value for filtering identified proteoform spectrum matches. + PSI:PI + + + + + + + + + + + + + + + P-value and E-value estimation using generating function. + MS + MS:1002923 + TopPIC:generating function + + + + + P-value and E-value estimation using generating function. + PSI:PI + + + + + + + + + + + + + + + Number of combined spectra. + MS + MS:1002924 + TopPIC:combined spectrum number + + + + + Number of combined spectra. + PSI:PI + + + + + + + + + The text file containing the information of common PTMs. + MS + MS:1002925 + TopPIC:mod file + + + + + The text file containing the information of common PTMs. + PSI:PI + + + + + + + + + + + + + + + Number of threads used in TopPIC. + MS + MS:1002926 + TopPIC:thread number + + + + + Number of threads used in TopPIC. + PSI:PI + + + + + + + + + + + + + + + Proteoform identification using TopFD feature file. + MS + MS:1002927 + TopPIC:use TopFD feature + + + + + Proteoform identification using TopFD feature file. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + TopPIC spectrum-level E-value. + MS + MS:1002928 + TopPIC:spectral E-value + + + + + TopPIC spectrum-level E-value. + PSI:PI + + + + + + + + + + + + + + + + TopPIC spectrum-level FDR. + MS + MS:1002929 + TopPIC:spectral FDR + + + + + TopPIC spectrum-level FDR. + PSI:PI + + + + + + + + + + + + + + + + TopPIC proteoform-level FDR. + MS + MS:1002930 + TopPIC:proteoform-level FDR + + + + + TopPIC proteoform-level FDR. + PSI:PI + + + + + + + + + + + + + + + + TopPIC spectrum-level p-value. + MS + MS:1002931 + TopPIC:spectral p-value + + + + + TopPIC spectrum-level p-value. + PSI:PI + + + + + + + + + + + + + + + Modification identification score. + MS + MS:1002932 + TopPIC:MIScore + + + + + Modification identification score. + PMID:27291504 + + + + + + + + + + + + + + + TopPIC:MIScore threshold. + MS + MS:1002933 + TopPIC:MIScore threshold + + + + + TopPIC:MIScore threshold. + PSI:PI + + + + + + + + + Search engine input parameters specific to TopMG. + MS + MS:1002934 + TopMG input parameter + + + + + Search engine input parameters specific to TopMG. + PSI:PI + + + + + + + + + Fixed modifications for TopMG searching. + MS + MS:1002935 + TopMG:fixed modification + + + + + Fixed modifications for TopMG searching. + PSI:PI + + + + + + + + + N-terminal forms of proteins allowed in TopMG searching. + MS + MS:1002936 + TopMG:N-term form + + + + + N-terminal forms of proteins allowed in TopMG searching. + PSI:PI + + + + + + + + + + + + + + + Error tolerance for precursor and fragment masses in PPM. + MS + MS:1002937 + TopMG:error tolerance + + + + + Error tolerance for precursor and fragment masses in PPM. + PSI:PI + + + + + + + + + + + + + + + Maximum value of the mass shift (in Dalton). + MS + MS:1002938 + TopMG:max shift + + + + + Maximum value of the mass shift (in Dalton). + PSI:PI + + + + + + + + + + + + + + + Spectrum-level cutoff type for filtering identified proteoform spectrum matches. + MS + MS:1002939 + TopMG:spectral cutoff type + + + + + Spectrum-level cutoff type for filtering identified proteoform spectrum matches. + PSI:PI + + + + + + + + + + + + + + + Spectrum-level cutoff value for filtering identified proteoform spectrum matches. + MS + MS:1002940 + TopMG:spectral cutoff value + + + + + Spectrum-level cutoff value for filtering identified proteoform spectrum matches. + PSI:PI + + + + + + + + + + + + + + + Proteoform-level cutoff type for filtering identified proteoform spectrum matches. + MS + MS:1002941 + TopMG:proteoform-level cutoff type + + + + + Proteoform-level cutoff type for filtering identified proteoform spectrum matches. + PSI:PI + + + + + + + + + + + + + + + Proteoform-level cutoff value for filtering identified proteoform spectrum matches. + MS + MS:1002942 + TopMG:proteoform-level cutoff value + + + + + Proteoform-level cutoff value for filtering identified proteoform spectrum matches. + PSI:PI + + + + + + + + + The text file containing the information of common PTMs. + MS + MS:1002943 + TopMG:mod file + + + + + The text file containing the information of common PTMs. + PSI:PI + + + + + + + + + + + + + + + Number of threads used in TopMG. + MS + MS:1002944 + TopMG:thread number + + + + + Number of threads used in TopMG. + PSI:PI + + + + + + + + + + + + + + + Proteoform identification using TopFD feature file. + MS + MS:1002945 + TopMG:use TopFD feature + + + + + Proteoform identification using TopFD feature file. + PSI:PI + + + + + + + + + + + + + + + Gap size in constructing proteoform graph. + MS + MS:1002946 + TopMG:proteoform graph gap size + + + + + Gap size in constructing proteoform graph. + PSI:PI + + + + + + + + + + + + + + + Maximum number of variable PTMs. + MS + MS:1002947 + TopMG:variable PTM number + + + + + Maximum number of variable PTMs. + PSI:PI + + + + + + + + + + + + + + + Maximum number of variable PTMs in a proteoform graph gap. + MS + MS:1002948 + TopMG:variable PTM number in proteoform graph gap + + + + + Maximum number of variable PTMs in a proteoform graph gap. + PSI:PI + + + + + + + + + + + + + + + Protein filtering using ASF-DIAGONAL method. + MS + MS:1002949 + TopMG:use ASF-DIAGONAL + + + + + Protein filtering using ASF-DIAGONAL method. + PMID:29327814 + + + + + + + + + + + + + + + + + + + + + + TopMG spectrum-level E-value. + MS + MS:1002950 + TopMG:spectral E-value + + + + + TopMG spectrum-level E-value. + PSI:PI + + + + + + + + + + + + + + + + TopMG spectrum-level FDR. + MS + MS:1002951 + TopMG:spectral FDR + + + + + TopMG spectrum-level FDR. + PSI:PI + + + + + + + + + + + + + + + + TopMG proteoform-level FDR. + MS + MS:1002952 + TopMG:proteoform-level FDR + + + + + TopMG proteoform-level FDR. + PSI:PI + + + + + + + + + + + + + + + + TopMG spectrum-level p-value. + MS + MS:1002953 + TopMG:spectral p-value + + + + + TopMG spectrum-level p-value. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry. + MS + MS:1002954 + collisional cross sectional area + + + + + Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry. + PSI:PI + + + + + + + + + + + + + + + Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'. + MS + MS:1002955 + hr-ms compound identification confidence level + + + + + Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'. + PMID:24476540 + + + + + + + + + + + + + + + A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'. + MS + MS:1002956 + isotopic ion MS peak + + + + + A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'. + PSI:PI + + + + + + + + + + + + + + + The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'. + MS + MS:1002957 + isotopomer MS peak + + + + + The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'. + PSI:PI + + + + + + + + + + + + + + + The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'. + MS + MS:1002958 + isotopologue MS peak + + + + + The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'. + PSI:PI + + + + + + + + + + + + + + + One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae. + MS + MS:1002959 + isomer + + + + + One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae. + https://goldbook.iupac.org/html/I/I03289.html + + + + + + + + + + + + + + + An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms. + MS + MS:1002960 + isotopomer + + + + + An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms. + https://goldbook.iupac.org/html/I/I03352.html + + + + + + + + + + + + + + + A molecular entity that differs only in isotopic composition (number of isotopic substitutions). + MS + MS:1002961 + isotopologue + + + + + A molecular entity that differs only in isotopic composition (number of isotopic substitutions). + https://goldbook.iupac.org/html/I/I03351.html + + + + + + + + + The arithmetic mean. + MS + MS:1002962 + mean + + + + + The arithmetic mean. + PSI:PI + + + + + + + + + The coefficient of variation. + MS + MS:1002963 + variation coefficient + + + + + The coefficient of variation. + PSI:PI + + + + + + + + + Lipidomics analysis software. + MS + MS:1002964 + lipidomics analysis software + + + + + Lipidomics analysis software. + PSI:PI + + + + + + + + + + Lipid Data Analyzer software for lipid quantification. + MS + MS:1002965 + Lipid Data Analyzer + + + + + Lipid Data Analyzer software for lipid quantification. + PMID:29058722 + + + + + + + + + The Lipid Data Analyzer native chrom format. + MS + MS:1002966 + chrom format + + + + + The Lipid Data Analyzer native chrom format. + PSI:PI + + + + + + + + + + Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets. + MS + MS:1002967 + LipidHunter + + + + + Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets. + PMID:28753264 + + + + + + + + + + Software for consensual cross-platform lipidomics. + MS + MS:1002968 + LipidXplorer + + + + + Software for consensual cross-platform lipidomics. + PMID:22272252 + + + + + + + + + + An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. + MS + MS:1002969 + LipidMatch + + + + + An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. + PMID:28693421 + + + + + + + + + + Open-source software for automated phospholipid tandem mass spectrometry identification. + MS + MS:1002970 + Greazy + + + + + Open-source software for automated phospholipid tandem mass spectrometry identification. + PMID:27186799 + + + + + + + + + + LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library. + MS + MS:1002971 + LipidBlast + + + + + LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library. + PMID:28660581 + + + + + + + + + + A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. + MS + MS:1002972 + Lipid-Pro + + + + + A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. + PMID:25433698 + + + + + + + + + + A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets. + MS + MS:1002973 + LipidFinder + + + + + A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets. + PMID:28405621 + + + + + + + + + + An integrated software package for high-confidence lipid identification. + MS + MS:1002974 + LipiDex + + + + + An integrated software package for high-confidence lipid identification. + PMID:29705063 + + + + + + + + + + An-open source software for identifying lipids in LC-MS/MS-based lipidomics data. + MS + MS:1002975 + LIQUID + + + + + An-open source software for identifying lipids in LC-MS/MS-based lipidomics data. + PMID:28158427 + + + + + + + + + + Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1). + MS + MS:1002976 + ALEX + + + + + Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1). + PMID:24244551 + + + + + + + + + + Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level. + MS + MS:1002977 + ALEX123 + + + + + Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level. + PMID:29786091 + + + + + + + + + + Software tool for the quantitative analysis of mass spectrometric lipidome data. + MS + MS:1002978 + LIMSA + + + + + Software tool for the quantitative analysis of mass spectrometric lipidome data. + PMID:17165823 + + + + + + + + + + Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers. + MS + MS:1002979 + LOBSTAHS + + + + + Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers. + PMID:27322848 + + + + + + + + + + Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species. + MS + MS:1002980 + LipidQA + + + + + Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species. + PMID:17720531 + + + + + + + + + The Proline software suite for mass spectrometry based proteomics. + MS + MS:1002981 + Proline + + + + + The Proline software suite for mass spectrometry based proteomics. + http://www.profiproteomics.fr/proline/ + + + + + + + + + PepNovo tool for de novo peptide sequencing. + MS + MS:1002982 + PepNovo + + + + + PepNovo tool for de novo peptide sequencing. + PMID:15858974 + + + + + + + + + pNovo tool for de novo peptide sequencing and identification using HCD spectra. + MS + MS:1002983 + pNovo + + + + + pNovo tool for de novo peptide sequencing and identification using HCD spectra. + PMID:20329752 + + + + + + + + + Novor real-time peptide de novo sequencing software tool. + MS + MS:1002984 + Novor + + + + + Novor real-time peptide de novo sequencing software tool. + PMID:26122521 + + + + + + + + + Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes. + MS + MS:1002985 + in-gel digestion + + + + + Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes. + PSI:PI + + + + + + + + + Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes. + MS + MS:1002986 + in-solution digestion + + + + + Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes. + PSI:PI + + + + + + + + + IdentiPy. + MS + MS:1002987 + IdentiPy + + + + + IdentiPy. + PMID:29682971 + https://bitbucket.org/levitsky/identipy + + + + + + + + + + + + + + + + + + + + + The IdentiPy result 'RHNS'. + MS + MS:1002988 + IdentiPy:RHNS + + + + + The IdentiPy result 'RHNS'. + PSI:PI + + + + + + + + + + + + + + + + + + + + + The IdentiPy result 'hyperscore'. + MS + MS:1002989 + IdentiPy:hyperscore + + + + + The IdentiPy result 'hyperscore'. + PSI:PI + + + + + + + + + ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra. + MS + MS:1002990 + ms_deisotope + + + + + ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra. + https://github.com/mobiusklein/ms_deisotope + + + + + + + + + python-psims, a library for generating mzML and mzIdentML. + MS + MS:1002991 + python-psims + + + + + python-psims, a library for generating mzML and mzIdentML. + https://github.com/mobiusklein/psims + + + + + + + + + + + + + + + + + + + + + + + + + + + Posterior error probability of the best identified peptide of the Andromeda search engine. + MS + MS:1002995 + Andromeda:PEP + + + + + Posterior error probability of the best identified peptide of the Andromeda search engine. + PSI:PI + + + + + + + + + Peak list file format of the Andromeda search engine. + MS + MS:1002996 + Andromeda:apl file format + + + + + Peak list file format of the Andromeda search engine. + PSI:PI + + + + + + + + + + + + + + + Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD). + MS + MS:1002997 + ProteomeXchange dataset identifier reanalysis number + + + + + Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD). + PSI:PI + + + + + + + + + Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS. + MS + MS:1002998 + LCMS-9030 + + + + + Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments LCMS-8060 MS. + MS + MS:1002999 + LCMS-8060 + + + + + Shimadzu Scientific Instruments LCMS-8060 MS. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments LCMS-8050 MS. + MS + MS:1003000 + LCMS-8050 + + + + + Shimadzu Scientific Instruments LCMS-8050 MS. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments LCMS-8045 MS. + MS + MS:1003001 + LCMS-8045 + + + + + Shimadzu Scientific Instruments LCMS-8045 MS. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments LCMS-8040 MS. + MS + MS:1003002 + LCMS-8040 + + + + + Shimadzu Scientific Instruments LCMS-8040 MS. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments LCMS-2020. + MS + MS:1003003 + LCMS-2020 + + + + + Shimadzu Scientific Instruments LCMS-2020. + PSI:MS + + + + + + + + + Bruker Daltonics' maXis II. + MS + MS:1003004 + maXis II + + + + + Bruker Daltonics' maXis II. + PSI:MS + + + + + + + + + Bruker Daltonics' timsTOF Pro. + MS + MS:1003005 + timsTOF Pro + + + + + Bruker Daltonics' timsTOF Pro. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1003006 + mean inverse reduced ion mobility array + + + + + Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1003007 + raw ion mobility array + + + + + Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1003008 + raw inverse reduced ion mobility array + + + + + Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + Shimadzu Biotech LCD file format. + MS + MS:1003009 + Shimadzu Biotech LCD format + + + + + Shimadzu Biotech LCD file format. + PSI:PI + + + + + + + + + + Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets. + MS + MS:1003010 + LPPtiger + + + + + Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets. + PMID:29123162 + + + + + + + + + Sequence-tag-based search engine pFind. + MS + MS:1003011 + pFind + + + + + Sequence-tag-based search engine pFind. + PMID:30295672 + + + + + + + + + + + + + + + Kernel mass spectral dot product scoring function. + MS + MS:1003012 + KSDP score + + + + + Kernel mass spectral dot product scoring function. + PMID:15044235 + + + + + + + + + i3-tms search engine and data-analysis software. + MS + MS:1003013 + i3tms + + + + + i3-tms search engine and data-analysis software. + PSI:PI + + + + + + + + + A database search-based peptide identification tool. + MS + MS:1003014 + MSFragger + + + + + A database search-based peptide identification tool. + PMID:28394336 + + + + + + + + + Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides. + MS + MS:1003015 + razor peptide + + + + + Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins. + MS + MS:1003016 + ProteinProphet:peptide weight + + + + + Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + Fraction of peptide evidence attributable to a group of proteins. + MS + MS:1003017 + ProteinProphet:peptide group weight + + + + + Fraction of peptide evidence attributable to a group of proteins. + PSI:PI + + + + + + + + + General proteomics processing toolkit for shotgun proteomics. + MS + MS:1003018 + Philosopher + + + + + General proteomics processing toolkit for shotgun proteomics. + https://philosopher.nesvilab.org/ + + + + + + + + + Representation of chromatographic pressure versus time. + MS + MS:1003019 + pressure chromatogram + + + + + Representation of chromatographic pressure versus time. + PSI:MS + + + + + + + + + Representation of the chromatographic flow rate versus time. + MS + MS:1003020 + flow rate chromatogram + + + + + Representation of the chromatographic flow rate versus time. + PSI:MS + + + + + + + + + + Post-translational modification which is assumed to be present at each instance of a residue type. + MS + MS:1003021 + Fixed modification + + + + + Post-translational modification which is assumed to be present at each instance of a residue type. + PSI:PI + + + + + + + + + + Post-translational modification which may or may not be present at a residue type. + MS + MS:1003022 + Variable modification + + + + + Post-translational modification which may or may not be present at a residue type. + PSI:PI + + + + + + + + + Cross-Linking MS search engine. + MS + MS:1003023 + OpenPepXL + + + + + Cross-Linking MS search engine. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + The OpenPepXL score for a cross-link spectrum match. + MS + MS:1003024 + OpenPepXL:score + + + + + The OpenPepXL score for a cross-link spectrum match. + PSI:PI + + + + + + + + + + + + + + A named element that is an attribute in a proteomics standards file. + MS + MS:1003025 + named element + + + + + A named element that is an attribute in a proteomics standards file. + PSI:PI + + + + + + + + + A named element that is an attribute in a mzIdentML file. + MS + MS:1003026 + named element in mzIdentML + + + + + A named element that is an attribute in a mzIdentML file. + PSI:PI + + + + + + + + + A named element that is an attribute in a mzML file. + MS + MS:1003027 + named element in mzML + + + + + A named element that is an attribute in a mzML file. + PSI:PI + + + + + + + + + Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS. + MS + MS:1003028 + Orbitrap Exploris 480 + + + + + Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS. + PSI:PI + + + + + + + + + Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. + MS + MS:1003029 + Orbitrap Eclipse + + + + + Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. + PSI:PI + + + + + + + + + + + + + + + Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'. + MS + MS:1003030 + Mascot:MinNumSigUniqueSeqs + + + + + Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'. + PSI:PI + + + + + + + + + + + + + + + Main identifier of a CPTAC dataset. + MS + MS:1003031 + CPTAC accession number + + + + + Main identifier of a CPTAC dataset. + PSI:PI + + + + + + + + + + + + + + + The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program. + MS + MS:1003032 + compound identification confidence code in MS-DIAL + + + + + The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program. + PMID:25938372 + http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL + + + + + + + + + + + + + + Non-inherent characteristic attributed to a molecular entity. + MS + MS:1003033 + molecular entity attribute + + + + + Non-inherent characteristic attributed to a molecular entity. + PSI:PI + + + + + + + + + Smallest constituent unit of ordinary matter that constitutes a chemical element. + MS + MS:1003034 + atom + + + + + Smallest constituent unit of ordinary matter that constitutes a chemical element. + https://en.wikipedia.org/wiki/Atom + + + + + + + + + Low molecular weight (< 900 daltons) organic compound that may regulate a biological process. + MS + MS:1003035 + small molecule + + + + + Low molecular weight (< 900 daltons) organic compound that may regulate a biological process. + https://en.wikipedia.org/wiki/Small_molecule + + + + + + + + + Small molecule that is the intermediate end product of metabolism. + MS + MS:1003036 + metabolite + + + + + Small molecule that is the intermediate end product of metabolism. + https://en.wikipedia.org/wiki/Metabolite + + + + + + + + + Nucleotide containing ribose as its pentose component. + MS + MS:1003037 + ribonucleotide + + + + + Nucleotide containing ribose as its pentose component. + https://en.wikipedia.org/wiki/Ribonucleotide + + + + + + + + + Monomer, or single unit, of DNA, or deoxyribonucleic acid. + MS + MS:1003038 + deoxyribonucleotide + + + + + Monomer, or single unit, of DNA, or deoxyribonucleic acid. + https://en.wikipedia.org/wiki/Deoxyribonucleotide + + + + + + + + + Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid. + MS + MS:1003039 + amino acid + + + + + Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid. + https://en.wikipedia.org/wiki/Amino_acid + + + + + + + + + Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule. + MS + MS:1003040 + monosaccharide + + + + + Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule. + https://en.wikipedia.org/wiki/Monosaccharide + + + + + + + + + Molecule composed of a chain of nucleotides. + MS + MS:1003041 + nucleic acid + + + + + Molecule composed of a chain of nucleotides. + https://en.wikipedia.org/wiki/Nucleic_acid + + + + + + + + + Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages. + MS + MS:1003042 + polysaccharide + + + + + Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages. + https://en.wikipedia.org/wiki/Polysaccharide + + + + + + + + + Number of amino acid residues in a peptide, commonly referred to as the peptide length. + MS + MS:1003043 + number of residues + + + + + Number of amino acid residues in a peptide, commonly referred to as the peptide length. + PSI:PI + + + + + + + + + Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not. + MS + MS:1003044 + number of missed cleavages + + + + + Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not. + PSI:PI + + + + + + + + + Process of mapping a peptide sequence to a protein sequence. + MS + MS:1003045 + peptide-to-protein mapping + + + + + Process of mapping a peptide sequence to a protein sequence. + PSI:PI + + + + + + + + + Nonphysical characteristic attributed to the result of peptide-to-protein mapping. + MS + MS:1003046 + peptide-to-protein mapping attribute + + + + + Nonphysical characteristic attributed to the result of peptide-to-protein mapping. + PSI:PI + + + + + + + + + + + + + + + Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence. + MS + MS:1003047 + protein sequence offset + + + + + Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence. + PSI:PI + + + + + + + + + + + + + + + Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules. + MS + MS:1003048 + number of enzymatic termini + + + + + Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules. + PSI:PI + + + + + + + + + Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations. + MS + MS:1003049 + peptidoform + + + + + Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations. + PSI:PI + + + + + + + + + + + + + + Non-inherent characteristic attributed to a peptidoform. + MS + MS:1003050 + peptidoform attribute + + + + + Non-inherent characteristic attributed to a peptidoform. + PSI:PI + + + + + + + + + Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'. + MS + parent ion + precursor + precursor ion + MS:1003051 + peptidoform ion + + + + + Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'. + PSI:PI + + + + + + + + + + + + + + Inherent or measurable characteristic of a peptidoform ion. + MS + MS:1003052 + peptidoform ion property + + + + + Inherent or measurable characteristic of a peptidoform ion. + PSI:PI + + + + + + + + + + + + + + + Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents. + MS + MS:1003053 + theoretical monoisotopic m/z + + + + + Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents. + PSI:PI + + + + + + + + + + + + + + + Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes. + MS + MS:1003054 + theoretical average m/z + + + + + Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes. + PSI:PI + + + + + + + + + Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species. + MS + MS:1003055 + adduct + + + + + Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species. + https://en.wikipedia.org/wiki/Adduct + + + + + + + + + + + + + + Physical measurable characteristic of an adduct ion. + MS + MS:1003056 + adduct ion property + + + + + Physical measurable characteristic of an adduct ion. + PSI:PI + + + + + + + + + + + + + + + Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run. + MS + MS:1003057 + scan number + + + + + Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run. + PSI:PI + + + + + + + + + + + + + + Inherent or measurable characteristic of a spectrum. + MS + MS:1003058 + spectrum property + + + + + Inherent or measurable characteristic of a spectrum. + PSI:PI + + + + + + + + + + + + + + + Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points. + MS + MS:1003059 + number of peaks + + + + + Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points. + PSI:PI + + + + + + + + + + + + + + + Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks. + MS + MS:1003060 + number of data points + + + + + Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks. + PSI:PI + + + + + + + + + + + + + + + Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection. + spectrum name + MS + MS:1003061 + library spectrum name + + + + + Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection. + PSI:PI + + + + + + + + + + + + + + + Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0. + MS + MS:1003062 + library spectrum index + + + + + Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0. + PSI:PI + + + + + + + + + + + + + + + PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library. + USI + MS + MS:1003063 + universal spectrum identifier + + + + + PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library. + PSI:PI + + + + + + + + + Non-inherent characteristic attributed to spectrum aggregation. + MS + MS:1003064 + spectrum aggregation attribute + + + + + Non-inherent characteristic attributed to spectrum aggregation. + PSI:PI + + + + + + + + + Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.). + MS + MS:1003065 + spectrum aggregation type + + + + + Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.). + PSI:PI + + + + + + + + + Spectrum that is not the result of some aggregation process. + MS + MS:1003066 + singleton spectrum + + + + + Spectrum that is not the result of some aggregation process. + PSI:PI + + + + + + + + + Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates. + MS + MS:1003067 + consensus spectrum + + + + + Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates. + PSI:PI + + + + + + + + + Spectrum that is considered the most representative from a pool of replicate spectra. + MS + MS:1003068 + best replicate spectrum + + + + + Spectrum that is considered the most representative from a pool of replicate spectra. + PSI:PI + + + + + + + + + + + + + + + Number of replicate spectra available for use during the aggregation process. + MS + MS:1003069 + number of replicate spectra available + + + + + Number of replicate spectra available for use during the aggregation process. + PSI:PI + + + + + + + + + + + + + + + Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm. + MS + MS:1003070 + number of replicate spectra used + + + + + Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm. + PSI:PI + + + + + + + + + Non-inherent characteristic attributed to spectrum aggregation. + MS + MS:1003071 + spectrum origin attribute + + + + + Non-inherent characteristic attributed to spectrum aggregation. + PSI:PI + + + + + + + + + Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.). + MS + MS:1003072 + spectrum origin type + + + + + Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.). + PSI:PI + + + + + + + + + Spectrum that originates from an analysis attempt of a single analyte species on an instrument. + MS + MS:1003073 + observed spectrum + + + + + Spectrum that originates from an analysis attempt of a single analyte species on an instrument. + PSI:PI + + + + + + + + + Spectrum that originates from a compututational algorithm that attempts to predict spectra. + MS + MS:1003074 + predicted spectrum + + + + + Spectrum that originates from a compututational algorithm that attempts to predict spectra. + PSI:PI + + + + + + + + + Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species. + MS + MS:1003075 + demultiplexed spectrum + + + + + Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species. + PSI:PI + + + + + + + + + Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features. + MS + MS:1003076 + uninterpreted spectrum + + + + + Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features. + PSI:PI + + + + + + + + + Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature. + MS + MS:1003077 + interpreted spectrum + + + + + Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature. + PSI:PI + + + + + + + + + + + + + + Non-inherent characteristic attributed to an interpreted spectrum. + MS + MS:1003078 + interpreted spectrum attribute + + + + + Non-inherent characteristic attributed to an interpreted spectrum. + PSI:PI + + + + + + + + + + + + + + + Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum. + MS + MS:1003079 + total unassigned intensity fraction + + + + + Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum. + PSI:PI + + + + + + + + + + + + + + + Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum. + MS + MS:1003080 + top 20 peak unassigned intensity fraction + + + + + Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum. + PSI:PI + + + + + + + + + + + + + + + + + + + + + Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML. + MS + MS:1003081 + unidentified modification monoisotopic mass delta + + + + + Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML. + PSI:PI + + + + + + + + + + Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors. + MS + MS:1003082 + MS-DIAL + + + + + Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors. + PMID:25938372 + + + + + + + + + Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file). + MS + MS:1003083 + raw data file + + + + + Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file). + PSI:MS + + + + + + + + + + + + + + + File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument. + MS + MS:1003084 + processed data file + + + + + File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument. + PSI:MS + + + + + + + + + + + + + + + + Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes. + MS + MS:1003085 + previous MSn-1 scan precursor intensity + + + + + Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes. + PSI:MS + + + + + + + + + + + + + + + + Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope. + MS + MS:1003086 + precursor apex intensity + + + + + Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope. + PSI:MS + + + + + + + + + Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available. + MS + MS:1003087 + supported by repository but incomplete data and/or metadata + + + + + Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available. + PSI:PI + + + + + + + + + Data array compression using mantissa bit truncation followed by zlib compression. + MS + MS:1003088 + truncation and zlib compression + + + + + Data array compression using mantissa bit truncation followed by zlib compression. + https://github.com/biospi/pwiz + + + + + + + + + Data array compression using mantissa bit truncation, delta prediction and zlib compression. + MS + MS:1003089 + truncation, delta prediction and zlib compression + + + + + Data array compression using mantissa bit truncation, delta prediction and zlib compression. + https://github.com/biospi/pwiz + + + + + + + + + Data array compression using mantissa bit truncation, linear prediction and zlib compression. + MS + MS:1003090 + truncation, linear prediction and zlib compression + + + + + Data array compression using mantissa bit truncation, linear prediction and zlib compression. + https://github.com/biospi/pwiz + + + + + + + + + + + + + + + + + + + + Settable parameter for a binary data compression event. + MS + MS:1003091 + binary data compression parameter + + + + + Settable parameter for a binary data compression event. + PSI:MS + + + + + + + + + + + + + + + Number of extraneous mantissa bits truncated to improve subsequent compression. + MS + MS:1003092 + number of mantissa bits truncated + + + + + Number of extraneous mantissa bits truncated to improve subsequent compression. + PSI:MS + + + + + + + + + + + + + + + Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues. + MS + MS:1003093 + Lys-N + + + + + Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues. + https://en.wikipedia.org/wiki/Lys-N + + + + + + + + + Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS. + MS + MS:1003094 + Orbitrap Exploris 240 + + + + + Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS. + PSI:PI + + + + + + + + + Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS. + MS + MS:1003095 + Orbitrap Exploris 120 + + + + + Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS. + PSI:PI + + + + + + + + + Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro. + MS + MS:1003096 + LTQ Orbitrap Velos Pro + + + + + Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro. + PSI:MS + + + + + + + + + + + + + + + The probability based MaxQuant protein group score. + MS + MS:1003097 + MaxQuant protein group-level score + + + + + The probability based MaxQuant protein group score. + PSI:MS + + + + + + + + + + + + + + + Peptide probability from Andromeda. + MS + MS:1003098 + Andromeda peptide PEP + + + + + Peptide probability from Andromeda. + PSI:MS + + + + + + + + + + + + + + + Peptide probability from MaxQuant-DIA algorithm. + MS + MS:1003099 + MaxQuant-DIA peptide PEP + + + + + Peptide probability from MaxQuant-DIA algorithm. + PSI:MS + + + + + + + + + + + + + + + PSM evidence score from MaxQuant-DIA algorithm. + MS + MS:1003100 + MaxQuant-DIA score + + + + + PSM evidence score from MaxQuant-DIA algorithm. + PSI:MS + + + + + + + + + + + + + + + PSM evidence PEP probability from MaxQuant-DIA algorithm. + MS + MS:1003101 + MaxQuant-DIA PEP + + + + + PSM evidence PEP probability from MaxQuant-DIA algorithm. + PSI:MS + + + + + + + + + + + + + + + Term for a comment field withing the NIST msp file format + MS + MS:1003102 + NIST msp comment + + + + + Term for a comment field withing the NIST msp file format + PSI:MS + + + + + + + + + Annotation format used for annotating individual spectrum ion peaks. + MS + MS:1003103 + ion annotation format + + + + + Annotation format used for annotating individual spectrum ion peaks. + PSI:MS + + + + + + + + + Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions. + MS + MS:1003104 + peptide ion annotation format + + + + + Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions. + PSI:MS + + + + + + + + + Annotation format designed specifically for cross-linked peptide ion peaks. + MS + MS:1003105 + cross-linked peptide ion annotation format + + + + + Annotation format designed specifically for cross-linked peptide ion peaks. + PSI:MS + + + + + + + + + Annotation format designed specifically for glycan ion peaks. + MS + MS:1003106 + glycan ion annotation format + + + + + Annotation format designed specifically for glycan ion peaks. + PSI:MS + + + + + + + + + Annotation format designed specifically for lipid ion peaks. + MS + MS:1003107 + lipid ion annotation format + + + + + Annotation format designed specifically for lipid ion peaks. + PSI:MS + + + + + + + + + + PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data. + MS + MS:1003108 + PatternLab + + + + + PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data. + PSI:MS + + + + + + + + + Identifying cross-linked peptides in complex protein mixtures + MS + MS:1003109 + SIM-XL + + + + + Identifying cross-linked peptides in complex protein mixtures + PSI:MS + + + + + + + + + + + + + + + + + + + + + SIM-XL identification search engine score + MS + MS:1003110 + SIM-XL score + + + + + SIM-XL identification search engine score + PSI:MS + + + + + + + + + Quantification of cross-linked peptides in complex protein mixtures + MS + MS:1003111 + QUIN-XL + + + + + Quantification of cross-linked peptides in complex protein mixtures + PSI:MS + + + + + + + + + Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. + MS + MS:1003112 + Orbitrap ID-X + + + + + Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. + PSI:MS + + + + + + + + + + + + + + + The OpenMS ConsesusID tool posterior error probability + MS + MS:1003113 + OpenMS:ConsensusID PEP + + + + + The OpenMS ConsesusID tool posterior error probability + PSI:MS + + + + + + + + + + + + + + + The score of the best PSM selected by the underlying identification tool + MS + MS:1003114 + OpenMS:Best PSM Score + + + + + The score of the best PSM selected by the underlying identification tool + PSI:MS + + + + + + + + + + + + + + + The OpenMS Target-decoy q-values at PSM level + MS + MS:1003115 + OpenMS:Target-decoy PSM q-value + + + + + The OpenMS Target-decoy q-values at PSM level + PSI:MS + + + + + + + + + + + + + + + The OpenMS Target-decoy q-values at peptide sequence level + MS + MS:1003116 + OpenMS:Target-decoy peptide q-value + + + + + The OpenMS Target-decoy q-values at peptide sequence level + PSI:MS + + + + + + + + + + + + + + + The OpenMS Target-decoy q-values at protein level + MS + MS:1003117 + OpenMS:Target-decoy protein q-value + + + + + The OpenMS Target-decoy q-values at protein level + PSI:MS + + + + + + + + + + A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework + MS + MS:1003118 + EPIFANY + + + + + A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework + PSI:MS + + + + + + + + + + + + + + + Protein Posterior probability calculated by EPIFANY protein inference algorithm + MS + MS:1003119 + EPIFANY:Protein posterior probability + + + + + Protein Posterior probability calculated by EPIFANY protein inference algorithm + PSI:MS + + + + + + + + + + + + + + + The data type LFQ intensity produced by OpenMS. + MS + MS:1003120 + OpenMS:LFQ intensity + + + + + The data type LFQ intensity produced by OpenMS. + PSI:MS + + + + + + + + + + + + + + + The data type LFQ spectral count produced by OpenMS. + MS + MS:1003121 + OpenMS:LFQ spectral count + + + + + The data type LFQ spectral count produced by OpenMS. + PSI:MS + + + + + + + + + Bruker Daltonics' rapiflex: MALDI TOF/TOF. + MS + MS:1003122 + rapifleX + + + + + Bruker Daltonics' rapiflex: MALDI TOF/TOF. + PSI:MS + + + + + + + + + Bruker Daltonics timsTOF series + MS + MS:1003123 + Bruker Daltonics timsTOF series + + + + + Bruker Daltonics timsTOF series + PSI:MS + + + + + + + + + Bruker Daltonics' timsTOF fleX + MS + MS:1003124 + timsTOF fleX + + + + + Bruker Daltonics' timsTOF fleX + PSI:MS + + + + + + + + + + + + + + + + + + + + + + ProSight spectrum-level Q-value. + MS + MS:1003125 + ProSight:spectral Q-value + + + + + ProSight spectrum-level Q-value. + PSI:MS + + + + + + + + + + + + + + + + + + + + + ProSight spectrum-level P-score. + MS + MS:1003126 + ProSight:spectral P-score + + + + + ProSight spectrum-level P-score. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + ProSight spectrum-level E-value. + MS + MS:1003127 + ProSight:spectral E-value + + + + + ProSight spectrum-level E-value. + PSI:MS + + + + + + + + + + + + + + + + + + + + + ProSight spectrum-level C-score. + MS + MS:1003128 + ProSight:spectral C-score + + + + + ProSight spectrum-level C-score. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + Estimation of the Q-value for proteoforms. + MS + MS:1003129 + proteoform-level Q-value + + + + + Estimation of the Q-value for proteoforms. + PSI:MS + + + + + + + + + + + + + + + + + + + + + ProSight proteoform-level Q-value. + MS + MS:1003130 + ProSight:proteoform Q-value + + + + + ProSight proteoform-level Q-value. + PSI:MS + + + + + + + + + Isoform level information. + MS + MS:1003131 + isoform-level identification attribute + + + + + Isoform level information. + PSI:MS + + + + + + + + + Identification confidence metric for a isoform. + MS + MS:1003132 + isoform-level identification statistic + + + + + Identification confidence metric for a isoform. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Estimation of the Q-value for isoforms. + MS + MS:1003133 + isoform-level Q-value + + + + + Estimation of the Q-value for isoforms. + PSI:MS + + + + + + + + + + + + + + + + + + + + + ProSight isoform-level Q-value. + MS + MS:1003134 + ProSight:isoform Q-value + + + + + ProSight isoform-level Q-value. + PSI:MS + + + + + + + + + + + + + + + + + + + + + ProSight protein-level Q-value. + MS + MS:1003135 + ProSight:protein Q-value + + + + + ProSight protein-level Q-value. + PSI:MS + + + + + + + + + Search engine input parameters specific to ProSight. + MS + MS:1003136 + ProSight input parameter + + + + + Search engine input parameters specific to ProSight. + PSI:MS + + + + + + + + + Search engine input parameters specific to TDPortal. + MS + MS:1003137 + TDPortal input parameter + + + + + Search engine input parameters specific to TDPortal. + PSI:MS + + + + + + + + + + + + + + + + If true, runs delta m mode in ProSight. + MS + MS:1003138 + ProSight:Run delta m mode + + + + + If true, runs delta m mode in ProSight. + PSI:MS + + + + + + + + + + + + + + + + If true, runs Subsequence Search mode in ProSight. + MS + MS:1003139 + ProSight:Run Subsequence Search mode + + + + + If true, runs Subsequence Search mode in ProSight. + PSI:MS + + + + + + + + + + + + + + + + If true, runs Annotated Proteoform Search mode in ProSight. + MS + MS:1003140 + ProSight:Run Annotated Proteoform Search mode + + + + + If true, runs Annotated Proteoform Search mode in ProSight. + PSI:MS + + + + + + + + + ProSight: Database search engine for top-down proteomics. + MS + MS:1003141 + ProSight + + + + + ProSight: Database search engine for top-down proteomics. + PSI:MS + + + + + + + + + TDPortal: Database search engine for top-down proteomics. + MS + MS:1003142 + TDPortal + + + + + TDPortal: Database search engine for top-down proteomics. + PSI:MS + + + + + + + + + + + + + + + A data array of mass values. + binary-data-type:MS:1000521 + binary-data-type:MS:1000523 + MS + MS:1003143 + mass array + + + + + A data array of mass values. + PSI:MS + + + + + binary-data-type:MS:1000521 + 32-bit float + + + + + binary-data-type:MS:1000523 + 64-bit float + + + + + + + + + SCIEX Triple Quad 7500. + MS + MS:1003144 + Triple Quad 7500 + + + + + SCIEX Triple Quad 7500. + PSI:MS + + + + + + + + + Cross-platform software to convert Thermo RAW files to a number of open formats. + MS + MS:1003145 + ThermoRawFileParser + + + + + Cross-platform software to convert Thermo RAW files to a number of open formats. + DOI:10.1021/acs.jproteome.9b00328 + PMID:31755270 + + + + + + + + + Python module that helps handling various proteomics data analysis tasks. + MS + MS:1003146 + pyteomics + + + + + Python module that helps handling various proteomics data analysis tasks. + DOI:10.1021/acs.jproteome.8b00717 + PMID:30576148 + + + + + + + + + + + + + + + Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet. + MS + MS:1003147 + PTMProphet probability + + + + + Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet. + DOI:10.1021/acs.jproteome.9b00205 + PMID:31290668 + + + + + + + + + + + + + + + PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet. + MS + MS:1003148 + PTMProphet mean best probability + + + + + PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet. + DOI:10.1021/acs.jproteome.9b00205 + PMID:31290668 + + + + + + + + + + + + + + + PTMProphet-computed PSM-specific normalized (0.0 – 1.0) measure of information content across all modifications of a specific type. + MS + MS:1003149 + PTMProphet normalized information content + + + + + PTMProphet-computed PSM-specific normalized (0.0 – 1.0) measure of information content across all modifications of a specific type. + DOI:10.1021/acs.jproteome.9b00205 + PMID:31290668 + + + + + + + + + + + + + + + PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type. + MS + MS:1003150 + PTMProphet information content + + + + + PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type. + DOI:10.1021/acs.jproteome.9b00205 + PMID:31290668 + + + + + + + + + + + + + + + SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity. + MS + MS:1003151 + SHA-256 + + + + + SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity. + PSI:MS + + + + + + + + + Shimadzu Scientific Instruments GCMS-QP2010SE. + MS + MS:1003152 + GCMS-QP2010SE + + + + + Shimadzu Scientific Instruments GCMS-QP2010SE. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1003153 + raw ion mobility drift time array + + + + + Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1003154 + deconvoluted ion mobility array + + + + + Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1003155 + deconvoluted inverse reduced ion mobility array + + + + + Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. + MS + MS:1003156 + deconvoluted ion mobility drift time array + + + + + Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum. + MS + MS:1003157 + scanning quadrupole position lower bound m/z array + + + + + Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum. + PSI:MS + + + + + + + + + + + + + + + + + + + + + Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum. + MS + MS:1003158 + scanning quadrupole position upper bound m/z array + + + + + Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum. + PSI:MS + + + + + + + + + Indicates an acquisition mode in which the isolation window is a full range, rather than a subset of the full range. + MS + MS:1003159 + isolation window full range + + + + + Indicates an acquisition mode in which the isolation window is a full range, rather than a subset of the full range. + PSI:MS + + + + + + + + + Proteomics Standards Initiative mzQC format for quality control data. + MS + MS:1003160 + mzQC format + + + + + Proteomics Standards Initiative mzQC format for quality control data. + PSI:MS + + + + + + + + + Grouping term for quality control data formats. + MS + MS:1003161 + quality control data format + + + + + Grouping term for quality control data formats. + PSI:MS + + + + + + + + + Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization. + PTXQC + MS + MS:1003162 + PTX-QC + + + + + Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization. + DOI:10.1021/acs.jproteome.5b00780 + PMID:26653327 + https://github.com/cbielow/PTXQC/ + + + + + + + + + + + + + + + The set of analyte identifiers that compose an interpretation of a spectrum. + MS + MS:1003163 + analyte mixture members + + + + + The set of analyte identifiers that compose an interpretation of a spectrum. + PSI:PI + + + + + + + + + QuaMeter IDFree software for QC metric calculation. + QuaMeter + MS + MS:1003164 + QuaMeter IDFree + + + + + QuaMeter IDFree software for QC metric calculation. + DOI:10.1021/ac4034455 + PMID:24494671 + + + + + + + + + iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files. + MS + MS:1003165 + iMonDB + + + + + iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files. + DOI:10.1021/acs.jproteome.5b00127 + PMID:25798920 + https://github.com/bittremieux/iMonDB + + + + + + + + + + + + + + + Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum + MS + MS:1003166 + assigned intensity fraction + + + + + Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum + PSI:PI + + + + + + + + + + + + + + + The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte + MS + MS:1003167 + MSn-1 isolation window precursor purity + + + + + The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte + PSI:PI + + + + + + + + + + + + + + + A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools. + MS + MS:1003168 + library spectrum comment + + + + + A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools. + PSI:PI + + + + + + + + + + + + + + + Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation + MS + MS:1003169 + proforma peptidoform sequence + + + + + Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation + PSI:PI + + + + + + + + + + + + + + A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments + MS + MS:1003170 + spectral library + + + + + A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments + PSI:PI + + + + + + + + + + + + + + An attribute of a spectral library + MS + MS:1003171 + spectral library attribute + + + + + An attribute of a spectral library + PSI:PI + + + + + + + + + + + + + + An entry in a spectral library representing a spectrum + MS + MS:1003172 + library spectrum + + + + + An entry in a spectral library representing a spectrum + PSI:PI + + + + + + + + + + + + + + + + + + + + + An attribute that takes on a numeric value + MS + MS:1003173 + numeric attribute + + + + + An attribute that takes on a numeric value + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + The maximum value for this attribute + MS + MS:1003174 + attribute maximum + + + + + The maximum value for this attribute + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + The minimum value for this attribute + MS + MS:1003175 + attribute minimum + + + + + The minimum value for this attribute + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + The arithmetic mean value for this attribute + MS + MS:1003176 + attribute mean + + + + + The arithmetic mean value for this attribute + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + The standard deviation (exact value of population, or estimate from sample) of this attribute + MS + MS:1003177 + attribute standard deviation + + + + + The standard deviation (exact value of population, or estimate from sample) of this attribute + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + The coefficient of variation of this attribute, i.e. standard deviation divided by the mean + MS + MS:1003178 + attribute coefficient of variation + + + + + The coefficient of variation of this attribute, i.e. standard deviation divided by the mean + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + The most appropriate summary value of the attribute, usually but not necessarily the mean + MS + MS:1003179 + attribute summary value + + + + + The most appropriate summary value of the attribute, usually but not necessarily the mean + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + The median of this attribute + MS + MS:1003180 + attribute median + + + + + The median of this attribute + PSI:PI + + + + + + + + + Combination of two or more dissociation methods that are known by a special term. + MS + MS:1003181 + combined dissociation method + + + + + Combination of two or more dissociation methods that are known by a special term. + PSI:PI + + + + + + + + + Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID). + ETciD + MS + MS:1003182 + electron-transfer/collision-induced dissociation + + + + + Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID). + PSI:PI + + + + + + + + + Waters oa-ToF based Synapt XS. + MS + MS:1003183 + Synapt XS + + + + + Waters oa-ToF based Synapt XS. + PSI:PI + + + + + + + + + Waters oa-ToF based SELECT SERIES Cyclic IMS. + MS + MS:1003184 + SELECT SERIES Cyclic IMS + + + + + Waters oa-ToF based SELECT SERIES Cyclic IMS. + PSI:PI + + + + + + + + + Waters oa-ToF based SELECT SERIES MRT. + MS + MS:1003185 + SELECT SERIES MRT + + + + + Waters oa-ToF based SELECT SERIES MRT. + PSI:PI + + + + + + + + + + + + + + + Version number of the [PSI] library format specification + MS + MS:1003186 + library format version + + + + + Version number of the [PSI] library format specification + PSI:PI + + + + + + + + + + + + + + + Short identifier for the library for easy reference, preferably but not necessarily globally unique + MS + MS:1003187 + library identifier + + + + + Short identifier for the library for easy reference, preferably but not necessarily globally unique + PSI:PI + + + + + + + + + + + + + + + A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library. + MS + MS:1003188 + library name + + + + + A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library. + PSI:PI + + + + + + + + + + + + + + + Extended free-text description of the library + MS + MS:1003189 + library description + + + + + Extended free-text description of the library + PSI:PI + + + + + + + + + + + + + + + Version number of the library, usually refering to a certain release of a continually updated library + MS + MS:1003190 + library version + + + + + Version number of the library, usually refering to a certain release of a continually updated library + PSI:PI + + + + + + + + + + + + + + + URI or URL that uniquely identifies the library + MS + MS:1003191 + library URI + + + + + URI or URL that uniquely identifies the library + PSI:PI + + + + + + + + + A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching + MS + MS:1003192 + decoy spectrum + + + + + A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching + PSI:PI + + + + + + + + + A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence. + MS + MS:1003193 + shuffle-and-reposition decoy spectrum + + + + + A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence. + PSI:PI + + + + + + + + + A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum. + MS + MS:1003194 + precursor shift decoy spectrum + + + + + A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum. + PSI:PI + + + + + + + + + A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform + MS + MS:1003195 + unnatural peptidoform decoy spectrum + + + + + A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform + PSI:PI + + + + + + + + + A decoy spectrum that is a real spectrum of a naturally occuring peptidoform of an unrelated species that should not be found in the sample + MS + MS:1003196 + unrelated species decoy spectrum + + + + + A decoy spectrum that is a real spectrum of a naturally occuring peptidoform of an unrelated species that should not be found in the sample + PSI:PI + + + + + + + + + + + + + + + URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/) + MS + MS:1003197 + license URI + + + + + URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/) + PSI:PI + + + + + + + + + + + + + + + Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work + MS + MS:1003198 + copyright notice + + + + + Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work + PSI:PI + + + + + + + + + + + + + + + Extended free-text description of the difference from the previous version + MS + MS:1003199 + change log + + + + + Extended free-text description of the difference from the previous version + PSI:PI + + + + + + + + + + + + + + + Version number of the software package used for library creation + MS + MS:1003200 + software version + + + + + Version number of the software package used for library creation + PSI:PI + + + + + + + + + Abstract term containing several different types of provenance information + MS + MS:1003201 + library provenance attribute + + + + + Abstract term containing several different types of provenance information + PSI:PI + + + + + + + + + + A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington + MS + MS:1003202 + BiblioSpec + + + + + A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington + PSI:PI + + + + + + + + + + + + + + + Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible. + MS + MS:1003203 + constituent spectrum file + + + + + Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible. + PSI:PI + + + + + + + + + + + + + + + Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible + MS + MS:1003204 + constituent identification file + + + + + Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible + PSI:PI + + + + + + + + + + + + + + + Source library URI which(at least) a subset of spectra were extracted from. + MS + MS:1003205 + constituent library file + + + + + Source library URI which(at least) a subset of spectra were extracted from. + PSI:PI + + + + + + + + + + + + + + + String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped + + MS + MS:1003206 + library creation log + + + + + String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped + + PSI:PI + + + + + + + + + + Library creation software + MS + MS:1003207 + library creation software + + + + + Library creation software + PSI:MS + + + + + + + + + + + + + + + + + + + + + + The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum. + MS + MS:1003208 + experimental precursor monoisotopic m/z + + + + + The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum. + MS + MS:1003209 + monoisotopic m/z deviation + + + + + The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum. + MS + MS:1003210 + average m/z deviation + + + + + The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum. + PSI:MS + + + + + + + + + A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library + MS + MS:1003211 + library spectrum attribute set + + + + + A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library + PSI:PI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A name to refer to a library attribute set + MS + MS:1003212 + library attribute set name + + + + + A name to refer to a library attribute set + PSI:PI + + + + + + + + + + Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated. + MS + MS:1003213 + mass spectrometry acquisition method + + + + + Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated. + PSI:MS + + + + + + + + + Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated. + MS + MS:1003214 + mass spectrometry acquisition method aspect + + + + + Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated. + PSI:MS + + + + + + + + + Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions. + DIA + MS + MS:1003215 + data-independent acquisition + + + + + Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions. + PSI:MS + + + + + + + + + Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.. + MS + MS:1003216 + dissociation of full mass range + + + + + Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.. + PSI:MS + + + + + + + + + Mass spectrometer data acquisition method wherein ????. + MS + MS:1003217 + dissociation of scanning quadrupole across a specified mass range + + + + + Mass spectrometer data acquisition method wherein ????. + PSI:MS + + + + + + + + + Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured. + MS + MS:1003218 + dissociation of sequential mass ranges + + + + + Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured. + PSI:MS + + + + + + + + + Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement. + MS + MS:1003219 + ion mobility separation + + + + + Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement. + PSI:MS + + + + + + + + + Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule. + MS + MS:1003220 + adduct deconvolution + + + + + Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule. + PSI:MS + + + + + + + + + Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run. + DDA + MS + MS:1003221 + data-dependent acquisition + + + + + Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run. + PSI:MS + + + + + + + + + Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte. + MS + MS:1003222 + ion mobility deconvolution + + + + + Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte. + PSI:MS + + + + + + + + + + + Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC. + MS + MS:1003224 + data independent acquisition from dissociation of sequential mass ranges + + + + + Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC. + PSI:MS + + + + + + + + + + + + Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF. + MS + MS:1003225 + data independent acquisition from dissociation of sequential mass ranges after ion mobility separation + + + + + Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF. + PSI:MS + + + + + + + + + + + + Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF. + MS + MS:1003226 + data independent acquisition from dissociation of full mass range after ion mobility separation + + + + + Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF. + PSI:MS + + + + + + + + + + + + Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID. + MS + MS:1003227 + data independent acquisition from dissociation of full mass range + + + + + Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID. + PSI:MS + + + + + + + + + + + Data independent mass spectrometer acquisition method wherein ???. An example of such an approach is Waters SONAR. + MS + MS:1003228 + data independent acquisition from dissociation of scanning quadrupole across mass range + + + + + Data independent mass spectrometer acquisition method wherein ???. An example of such an approach is Waters SONAR. + PSI:MS + + + + + + + + + Bruker Daltonics' timsTOF. + MS + MS:1003229 + timsTOF + + + + + Bruker Daltonics' timsTOF. + PSI:MS + + + + + + + + + Bruker Daltonics' timsTOF Pro 2. + MS + MS:1003230 + timsTOF Pro 2 + + + + + Bruker Daltonics' timsTOF Pro 2. + PSI:MS + + + + + + + + + Bruker Daltonics' timsTOF SCP. + MS + MS:1003231 + timsTOF SCP + + + + + Bruker Daltonics' timsTOF SCP. + PSI:MS + + + + + + + + + + + comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB). + MS + MS:1003232 + PeakForest + + + + + comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB). + https://peakforest.org/ + + + + + + + + + + + + + + An attribute that describes information about an entry in a spectral library + MS + MS:1003234 + library spectrum attribute + + + + + An attribute that describes information about an entry in a spectral library + PSI:PI + + + + + + + + + The ionization of analytes from a piece of paper by applying a solvent and voltage. + MS + MS:1003235 + paper spray ionization + + + + + The ionization of analytes from a piece of paper by applying a solvent and voltage. + PSI:MS + + + + + + + + + + + + + + + An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library. + MS + MS:1003237 + library spectrum key + + + + + An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library. + PSI:PI + + + + + + + + + A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library + MS + MS:1003238 + library analyte attribute set + + + + + A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library + PSI:PI + + + + + + + + + A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library + MS + MS:1003239 + library interpretation attribute set + + + + + A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library + PSI:PI + + + + + + + + + A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores + MS + MS:1003240 + peak intensity transform + + + + + A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores + PSI:PI + + + + + + + + + A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots + MS + MS:1003241 + square root transform + + + + + A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots + PSI:PI + + + + + + + + + A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks + MS + MS:1003242 + rank transform + + + + + A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks + PSI:PI + + + + + + + + + + + + + + + The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule’s mass plus the mass of a proton) + MS + MS:1003243 + adduct ion mass + + + + + The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule’s mass plus the mass of a proton) + PSI:PI + + + + + + + + + + + + + + + Accession number (e.g. in PeptideAtlas) of the peptide sequence + MS + MS:1003244 + peptide accession number + + + + + Accession number (e.g. in PeptideAtlas) of the peptide sequence + PSI:PI + + + + + + + + + Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS. + MS + MS:1003245 + Q Exactive UHMR + + + + + Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS. + PSI:PI + + + + + + + + + Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons. + UVPD + MS + MS:1003246 + ultraviolet photodissociation + + + + + Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons. + PSI:MS + + + + + + + + + A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation. + NETD + MS + MS:1003247 + negative electron transfer dissociation + + + + + A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation. + DOI:10.1016/j.jasms.2005.01.015 + PSI:MS + + + + + + + + + Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation. + PTR + MS + MS:1003248 + proton transfer reaction + + + + + Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation. + DOI:10.1002/mas.20048 + PSI:MS + + + + + + + + + Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte. + PTCR + MS + MS:1003249 + proton transfer charge reduction + + + + + Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence. + MS + MS:1003250 + count of identified peptidoforms + + + + + The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence. + PSI:PI + + + + + + + + + + + + + + + + + + + + + + The number of spectra that pass the threshold to be considered identified with sufficient confidence. + MS + MS:1003251 + count of identified spectra + + + + + The number of spectra that pass the threshold to be considered identified with sufficient confidence. + PSI:PI + + + + + + + + + Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer. + MS + MS:1003252 + Xevo G2-XS QTof + + + + + Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer. + PSI:PI + + + + + + + + + + A universal software for data-independent acquisition (DIA) proteomics data processing + MS + MS:1003253 + DIA-NN + + + + + A universal software for data-independent acquisition (DIA) proteomics data processing + PMID:31768060 + https://github.com/vdemichev/DiaNN + + + + + + + + + + + + + + An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. + MS + MS:1003254 + peak attribute + + + + + An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. + PSI:PI + + + + + + + + + For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. + MS + MS:1003255 + pre-decharged charge state + + + + + For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. + PSI:PI + + + + + + + + + + + + + + Non-inherent characteristic attributed to a peptidoform + MS + MS:1003256 + peptidoform ion attribute + + + + + Non-inherent characteristic attributed to a peptidoform + PSI:PI + + + + + + + + + A link from one spectrum to another spectrum of interest + MS + MS:1003257 + library spectrum cross reference + + + + + A link from one spectrum to another spectrum of interest + PSI:PI + + + + + + + + + A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. + MS + MS:1003258 + related spectrum + + + + + A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. + PSI:PI + + + + + + + + + + + + + + + A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. + MS + MS:1003259 + related spectrum keys + + + + + A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. + PSI:PI + + + + + + + + + + + + + + + A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier + MS + MS:1003260 + related spectrum USI + + + + + A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier + PSI:PI + + + + + + + + + + + + + + + + + + + + A free-text string describing the related spectrum and/or its relationship to this spectrum + MS + MS:1003261 + related spectrum description + + + + + A free-text string describing the related spectrum and/or its relationship to this spectrum + PSI:PI + + + + + + + + + A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion. + MS + MS:1003262 + similar spectrum + + + + + A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion. + PSI:PI + + + + + + + + + + + + + + + A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. + MS + MS:1003263 + similar spectrum keys + + + + + A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. + PSI:PI + + + + + + + + + + + + + + + A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier + MS + MS:1003264 + similar spectrum USI + + + + + A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier + PSI:PI + + + + + + + + + + + + + + A group of spectra that are spectrally similar to each other + MS + MS:1003265 + spectrum cluster + + + + + A group of spectra that are spectrally similar to each other + PSI:PI + + + + + + + + + + + + + + A non-inherent characteristic of a spectrum cluster + MS + MS:1003266 + spectrum cluster attribute + + + + + A non-inherent characteristic of a spectrum cluster + PSI:PI + + + + + + + + + + + + + + + An ordinal number uniquely identifying a spectrum cluster. It should start with 1. + MS + MS:1003267 + spectrum cluster key + + + + + An ordinal number uniquely identifying a spectrum cluster. It should start with 1. + PSI:PI + + + + + + + + + + + + + + + A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library. + MS + MS:1003268 + spectrum cluster member spectrum keys + + + + + A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library. + PSI:PI + + + + + + + + + + + + + + + A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier. + MS + MS:1003269 + spectrum cluster member USI + + + + + A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier. + PSI:PI + + + + + + + + + A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type. + MS + MS:1003270 + proforma peptidoform ion notation + + + + + A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type. + PSI:PI + + + + + + + + + + + + + + The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum. + MS + MS:1003271 + peak annotation + + + + + The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum. + PSI:PI + + + + + + + + + + + + + + + + + + + + A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'. + MS + MS:1003272 + peak annotation string + + + + + A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'. + PSI:PI + + + + + + + + + + + + + + + + + + + + A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'. + MS + MS:1003273 + peak annotation confidence + + + + + A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'. + PSI:PI + + + + + + + + + A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1. + MS + MS:1003274 + peak annotation confidence metric + + + + + A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1. + PSI:PI + + + + + + + + + + + + + + + A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value + MS + MS:1003275 + other attribute name + + + + + A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name + MS + MS:1003276 + other attribute value + + + + + A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name + PSI:MS + + + + + + + + + Value range for signed normalized score values. + MS + MS:1003277 + value between -1 and 1 inclusive + + + + + Value range for signed normalized score values. + PSI:PI + + + + + + + + + A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte. + MS + MS:1003278 + m/z variability of peak + + + + + A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte. + PSI:PI + + + + + + + + + + + + + + + The frequency at which this peak is observed among replicate spectra of the same analyte. + MS + MS:1003279 + observation frequency of peak + + + + + The frequency at which this peak is observed among replicate spectra of the same analyte. + PSI:PI + + + + + + + + + A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte. + MS + MS:1003280 + intensity variability of peak + + + + + A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte. + PSI:PI + + + + + + + + + Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/. + MS + MS:1003281 + Casanovo + + + + + Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/. + https://github.com/Noble-Lab/casanovo/ + + + + + + + + + Bruker TSF raw file format. + MS + MS:1003282 + Bruker TSF format + + + + + Bruker TSF raw file format. + PSI:MS + + + + + + + + + Native format defined by frame=xsd:nonNegativeInteger. + MS + MS:1003283 + Bruker TSF nativeID format + + + + + Native format defined by frame=xsd:nonNegativeInteger. + PSI:MS + + + + + + + + + + + + + + + Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation. + MS + MS:1003284 + Bruker TSF nativeID format, combined spectra + + + + + Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation. + PSI:PI + + + + + + + + + + + + + + + The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte. + MS + MS:1003285 + standard deviation of m/z values of peak among replicates + + + + + The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte. + PSI:PI + + + + + + + + + + + + + + + The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte. + MS + MS:1003286 + coefficient of variation of intensity of peak among replicates + + + + + The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte. + PSI:PI + + + + + + + + + + + + + + + The standard deviation of the intensities of this peak among the replicate spectra of the same analyte. + MS + MS:1003287 + standard deviation of intensity of peak among replicates + + + + + The standard deviation of the intensities of this peak among the replicate spectra of the same analyte. + PSI:PI + + + + + + + + + + + + + + + The number of unassigned peaks in the spectrum. + MS + MS:1003288 + number of unassigned peaks + + + + + The number of unassigned peaks in the spectrum. + NIST + + + + + + + + + + + + + + + The intensity of the highest unassigned peak in the spectrum. + MS + MS:1003289 + intensity of highest unassigned peak + + + + + The intensity of the highest unassigned peak in the spectrum. + NIST + + + + + + + + + + + + + + + The number of unassigned peaks among the most intense 20 peaks in the spectrum. + MS + MS:1003290 + number of unassigned peaks among top 20 peaks + + + + + The number of unassigned peaks among the most intense 20 peaks in the spectrum. + NIST + + + + + + + + + + + + + + + Luciphor phosphosite localization score + MS + MS:1003291 + Luciphor deltaScore + + + + + Luciphor phosphosite localization score + PSI:MS + + + + + + + + + Thermo Scientific TSQ Altis Plus Triple Quadrupole MS. + MS + MS:1003292 + TSQ Altis Plus + + + + + Thermo Scientific TSQ Altis Plus Triple Quadrupole MS. + PSI:PI + + + + + + + + + SCIEX ZenoTOF 7600. + MS + MS:1003293 + ZenoTOF 7600 + + + + + SCIEX ZenoTOF 7600. + PSI:MS + + + + + + + + + A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. + EAD + MS + MS:1003294 + electron activated dissociation + + + + + A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. + PSI:MS + + + + + + + + + Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum. + MS + MS:1003295 + summary statistics of replicates + + + + + Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum. + PSI:PI + + + + + + + + + + + + + + + The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name' + MS + MS:1003296 + number of replicates spectra used from source + + + + + The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name' + PSI:PI + + + + + + + + + A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum. + MS + MS:1003297 + contributing replicate spectrum + + + + + A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum. + PSI:PI + + + + + + + + + + + + + + A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys. + MS + MS:1003298 + contributing replicate spectrum keys + + + + + A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys. + PSI:PI + + + + + + + + + + + + + + A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers. + MS + MS:1003299 + contributing replicate spectrum USI + + + + + A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers. + PSI:PI + + + + + + + + + + + + + + Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte. + MS + MS:1003300 + spectrum match + + + + + Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte. + PSI:PI + + + + + + + + + Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence. + PSM + MS + MS:1003301 + peptide-spectrum match + + + + + Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence. + PSI:PI + + + + + + + + + Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering. + SSM + MS + MS:1003302 + spectrum-spectrum match + + + + + Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering. + PSI:PI + + + + + + + + + + + + + + + A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone. + MS + MS:1003303 + spectral similarity + + + + + A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone. + PSI:PI + + + + + + + + + + + + + + + The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity. + cosine similarity + MS + MS:1003304 + spectral dot product + + + + + The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity. + PSI:PI + + + + + + + + + + + + + + + The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space. + MS + MS:1003305 + spectral Euclidean distance + + + + + The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space. + PSI:PI + + + + + + + + + + + + + + + The number of peaks with closely matching m/z values that are common to two spectra. + MS + MS:1003306 + shared peak count + + + + + The number of peaks with closely matching m/z values that are common to two spectra. + PSI:PI + + + + + + + + + + + + + + + The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi. + MS + MS:1003307 + normalized spectral angle + + + + + The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi. + https://doi.org/10.1074/mcp.O113.036475 + + + + + + + + + + + + + + + The Pearson's rho statistic between a pair of points representing two vectorized spectra. + MS + MS:1003308 + spectral Pearson correlation + + + + + The Pearson's rho statistic between a pair of points representing two vectorized spectra. + PSI:PI + + + + + + + + + + + + + + + The number of spectra in a spectrum cluster. + MS + MS:1003320 + spectrum cluster size + + + + + The number of spectra in a spectrum cluster. + PSI:PI + + + + + + + + + Summary statistics of an attribute among all spectra of a spectrum cluster. + MS + MS:1003321 + summary statistics of clustered spectra + + + + + Summary statistics of an attribute among all spectra of a spectrum cluster. + PSI:PI + + + + + + + + + + + + + + + Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not. + MS + MS:1003322 + spectrum cluster best representative + + + + + Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not. + PSI:PI + + + + + + + + + + + + + + + Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not. + MS + MS:1003323 + spectrum cluster consensus spectrum + + + + + Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not. + PSI:PI + + + + + + + + + + + + + + + + Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum. + MS + MS:1003324 + spectral dot product to aggregated spectrum + + + + + Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum. + PSI:PI + + + + + + + + + + + + + + PSI Quality Control controlled vocabulary term. + MS + MS:4000000 + PSI-MS CV Quality Control Vocabulary + + + + + PSI Quality Control controlled vocabulary term. + PSI:MS + + + + + + + + + + + + + + Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations. + MS + MS:4000001 + QC metric + + + + + Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations. + PSI:MS + + + + + + + + + + + + + + The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix. + MS + MS:4000002 + QC metric value type + + + + + The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix. + PSI:MS + + + + + + + + + Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). + MS + MS:4000003 + single value + + + + + Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). + PSI:MS + + + + + + + + + Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable). + MS + MS:4000004 + n-tuple + + + + + Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable). + PSI:MS + + + + + + + + + Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). + MS + MS:4000005 + The actual structure of the table is defined in the mzQC specification document. In short: it must have at least one column, and MAY have optional columns. + table + + + + + Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). + PSI:MS + + + + + + + + + A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable). + MS + MS:4000006 + The actual structure of the matrix is defined in the mzQC specification document. + matrix + + + + + A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable). + PSI:MS + + + + + + + + + + + + + + Categorization of the QC metric. + MS + MS:4000007 + QC metric category + + + + + Categorization of the QC metric. + PSI:MS + + + + + + + + + QC metric based on identification results. + MS + MS:4000008 + ID based metric + + + + + QC metric based on identification results. + PSI:MS + + + + + + + + + QC metric not based on identification results. + MS + MS:4000009 + ID free metric + + + + + QC metric not based on identification results. + PSI:MS + + + + + + + + + QC metric based on quantification results. + MS + MS:4000010 + quantification based metric + + + + + QC metric based on quantification results. + PSI:MS + + + + + + + + + QC metric calculated from a single run (e.g. one .raw file). + MS + MS:4000012 + single run based metric + + + + + QC metric calculated from a single run (e.g. one .raw file). + PSI:MS + + + + + + + + + QC metric calculated from multiple runs (e.g. multiple .raw files). + MS + MS:4000013 + multiple runs based metric + + + + + QC metric calculated from multiple runs (e.g. multiple .raw files). + PSI:MS + + + + + + + + + QC metric calculated from a single spectrum. + MS + MS:4000014 + single spectrum based metric + + + + + QC metric calculated from a single spectrum. + PSI:MS + + + + + + + + + QC metric calculated from multiple spectra. + MS + MS:4000015 + multiple spectra based metric + + + + + QC metric calculated from multiple spectra. + PSI:MS + + + + + + + + + QC metric related to retention time. + MS + MS:4000016 + retention time metric + + + + + QC metric related to retention time. + PSI:MS + + + + + + + + + QC metric related to a chromatogram. + MS + MS:4000017 + chromatogram metric + + + + + QC metric related to a chromatogram. + PSI:MS + + + + + + + + + QC metric related to an extracted ion chromatogram. + MS + MS:4000018 + XIC metric + + + + + QC metric related to an extracted ion chromatogram. + PSI:MS + + + + + + + + + QC metric related to the mass spectrometry acquisition. + MS + MS:4000019 + MS metric + + + + + QC metric related to the mass spectrometry acquisition. + PSI:MS + + + + + + + + + QC metric related to events in the ion source. + MS + MS:4000020 + ion source metric + + + + + QC metric related to events in the ion source. + PSI:MS + + + + + + + + + QC metric based on MS1 events. + MS + MS:4000021 + MS1 metric + + + + + QC metric based on MS1 events. + PSI:MS + + + + + + + + + QC metric based on MS2 events. + MS + MS:4000022 + MS2 metric + + + + + QC metric based on MS2 events. + PSI:MS + + + + + + + + + QC metric related to the sample preparation. + MS + MS:4000023 + sample preparation metric + + + + + QC metric related to the sample preparation. + PSI:MS + + + + + + + + + QC metric related to measurements of the ambient environment, such as the laboratory. + MS + MS:4000024 + environment metric + + + + + QC metric related to measurements of the ambient environment, such as the laboratory. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC. + XIC-WideFrac + MS + MS:4000050 + This metric characterises the distribution of precursor peak widths, much as the N50 characterises contig sizes in genome assembly. + XIC50 fraction + + + + + The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC. + PSI:MS + + + + + XIC-WideFrac + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of of XIC-FWHM-Q1,Q2,Q3. + MS + XIC-FWHM-Q1 + XIC-FWHM-Q2 + XIC-FWHM-Q3 + MS:4000051 + XIC-FWHM quantiles + + + + + The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of of XIC-FWHM-Q1,Q2,Q3. + PSI:MS + + + + + XIC-FWHM-Q1 + PMID:24494671 + + + + + XIC-FWHM-Q2 + PMID:24494671 + + + + + XIC-FWHM-Q3 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. + MS + XIC-Height-Q2 + XIC-Height-Q3 + XIC-Height-Q4 + MS:4000052 + XIC-Height quartile ratios + + + + + The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3. + PSI:MS + + + + + XIC-Height-Q2 + PMID:24494671 + + + + + XIC-Height-Q3 + PMID:24494671 + + + + + XIC-Height-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The retention time duration of the chromatography in seconds. + MS + RT-Duration + MS:4000053 + chromatography duration + + + + + The retention time duration of the chromatography in seconds. + PSI:MS + + + + + RT-Duration + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The interval when the respective quarter of the TIC accumulates divided by retention time duration. + MS + RT-TIC-Q1 + RT-TIC-Q2 + RT-TIC-Q3 + RT-TIC-Q4 + MS:4000054 + TIC quarters RT fraction + + + + + The interval when the respective quarter of the TIC accumulates divided by retention time duration. + PSI:QC + + + + + RT-TIC-Q1 + PMID:24494671 + + + + + RT-TIC-Q2 + PMID:24494671 + + + + + RT-TIC-Q3 + PMID:24494671 + + + + + RT-TIC-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. + MS + RT-MS-Q1 + RT-MS-Q2 + RT-MS-Q3 + RT-MS-Q4 + MS:4000055 + MS1 quarter RT fraction + + + + + The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration. + PSI:QC + + + + + RT-MS-Q1 + PMID:24494671 + + + + + RT-MS-Q2 + PMID:24494671 + + + + + RT-MS-Q3 + PMID:24494671 + + + + + RT-MS-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. + MS + RT-MSMS-Q1 + RT-MSMS-Q2 + RT-MSMS-Q3 + RT-MSMS-Q4 + MS:4000056 + MS2 quarter RT fraction + + + + + The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration. + PSI:QC + + + + + RT-MSMS-Q1 + PMID:24494671 + + + + + RT-MSMS-Q2 + PMID:24494671 + + + + + RT-MSMS-Q3 + PMID:24494671 + + + + + RT-MSMS-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 + MS + MS1-TIC-Change-Q2 + MS1-TIC-Change-Q3 + MS1-TIC-Change-Q4 + MS:4000057 + MS1 TIC-change quartile ratios + + + + + The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3 + PSI:MS + + + + + MS1-TIC-Change-Q2 + PMID:24494671 + + + + + MS1-TIC-Change-Q3 + PMID:24494671 + + + + + MS1-TIC-Change-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. + MS + MS1-TIC-Q2 + MS1-TIC-Q3 + MS1-TIC-Q4 + MS:4000058 + MS1 TIC quartile ratios + + + + + The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3. + PSI:MS + + + + + MS1-TIC-Q2 + PMID:24494671 + + + + + MS1-TIC-Q3 + PMID:24494671 + + + + + MS1-TIC-Q4 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of MS1 events in the run. + MS1-Count + MS + MS:4000059 + number of MS1 spectra + + + + + The number of MS1 events in the run. + PSI:MS + + + + + MS1-Count + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of MS2 events in the run. + MS2-Count + MS + MS:4000060 + number of MS2 spectra + + + + + The number of MS2 events in the run. + PSI:MS + + + + + MS2-Count + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode. + MS + MS1-Density-Q1 + MS1-Density-Q2 + MS1-Density-Q3 + MS:4000061 + MS1 density quantiles + + + + + The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode. + PSI:MS + + + + + MS1-Density-Q1 + PMID:24494671 + + + + + MS1-Density-Q2 + PMID:24494671 + + + + + MS1-Density-Q3 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode. + MS + MS2-Density-Q1 + MS2-Density-Q2 + MS2-Density-Q3 + MS:4000062 + MS2 density quantiles + + + + + The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode. + PSI:MS + + + + + MS2-Density-Q1 + PMID:24494671 + + + + + MS2-Density-Q2 + PMID:24494671 + + + + + MS2-Density-Q3 + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher. + MS2-PrecZ-1 + MS2-PrecZ-2 + MS2-PrecZ-3 + MS2-PrecZ-4 + MS2-PrecZ-5 + MS2-PrecZ-more + MS + IS-3A + IS-3B + IS-3C + MS:4000063 + the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2. + MS2 known precursor charges fractions + + + + + The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher. + PSI:MS + + + + + MS2-PrecZ-1 + PMID:24494671 + + + + + MS2-PrecZ-2 + PMID:24494671 + + + + + MS2-PrecZ-3 + PMID:24494671 + + + + + MS2-PrecZ-4 + PMID:24494671 + + + + + MS2-PrecZ-5 + PMID:24494671 + + + + + MS2-PrecZ-more + PMID:24494671 + + + + + IS-3A + PMID:19837981 + + + + + IS-3B + PMID:19837981 + + + + + IS-3C + PMID:19837981 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states. + MS + MS2-PrecZ-likely-1 + MS2-PrecZ-likely-multi + MS:4000064 + MS2 unknown and likely precursor charges fractions + + + + + The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states. + PSI:MS + + + + + MS2-PrecZ-likely-1 + PMID:24494671 + + + + + MS2-PrecZ-likely-multi + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Fastest frequency for MS level 1 collection + MS1-Freq-Max + MS + MS:4000065 + Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. + fastest frequency for MS level 1 collection + + + + + Fastest frequency for MS level 1 collection + PSI:MS + + + + + MS1-Freq-Max + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Fastest frequency for MS level 2 collection + MS2-Freq-Max + MS + MS:4000066 + Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. + fastest frequency for MS level 2 collection + + + + + Fastest frequency for MS level 2 collection + PSI:MS + + + + + MS2-Freq-Max + PMID:24494671 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds. + MS + MS:4000067 + MS run duration + + + + + The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well. + MS + MS:4000068 + spectra half-TIC + + + + + The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Upper and lower limit of m/z precursor values at which MSn spectra are recorded. + MS + MS:4000069 + m/z acquisition range + + + + + Upper and lower limit of m/z precursor values at which MSn spectra are recorded. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Upper and lower limit of retention time at which spectra are recorded. + MS + MS:4000070 + retention time acquisition range + + + + + Upper and lower limit of retention time at which spectra are recorded. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of chromatograms recorded for the run. + MS + MS:4000071 + number of chromatograms + + + + + The number of chromatograms recorded for the run. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum. + MS + MS:4000072 + observed mass accuracy + + + + + Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum. + PSI:MS + + + + + + + + + A QC metric based on a QC sample of known content. + MS + MS:4000073 + QC sample metric + + + + + A QC metric based on a QC sample of known content. + PSI:MS + + + + + + + + + A QC metric based on a QC sample of known and high complexity content. + MS + MS:4000074 + high complexity QC sample metric + + + + + A QC metric based on a QC sample of known and high complexity content. + PSI:MS + + + + + + + + + A QC metric based on a QC sample of known and low complexity content. + MS + MS:4000075 + low complexity QC sample metric + + + + + A QC metric based on a QC sample of known and low complexity content. + PSI:MS + + + + + + + + + A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design. + MS + MS:4000076 + Expected peptides from QC2 sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR' + QC2 sample metric + + + + + A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design. + PMID:23088386 + PMID:29324744 + PSI:MS + + + + + + + + + A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design). + MS + MS:4000077 + Expected peptides from QC1 sample measurement are: 'LVNELTEFAK','HLVDEPQNLIK','VPQVSTPTLVEVSR','EAC(Carbamidomethyl)FAVEGPK','EYEATLEEC(Carbamidomethyl)C(Carbamidomethyl)AK','EC(Carbamidomethyl)C(Carbamidomethyl)HGDLLEC(Carbamidomethyl)ADDR','SLHTLFGDELC(Carbamidomethyl)K','TC(Carbamidomethyl)VADESHAGC(Carbamidomethyl)EK','YIC(Carbamidomethyl)DNQDTISSK','NEC(Carbamidomethyl)FLSHK' + QC1 sample metric + + + + + A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design). + PMID:23088386 + PMID:29324744 + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected. + MS + MS:4000078 + QC2 sample mass accuracies + + + + + Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected. + MS + MS:4000079 + QC2 sample intensities + + + + + Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected. + PSI:MS + + + + + + + + + + + + + + QC terms associated but not directly metrics themselves. + MS + MS:4000080 + QC non-metric term + + + + + QC terms associated but not directly metrics themselves. + PSI:MS + + + + + + + + + + + + + + + Data from the first principal component of a PCA. + 1st PC + MS + MS:4000081 + first principal component + + + + + Data from the first principal component of a PCA. + PSI:MS + + + + + + + + + + + + + + + Data from the second principal component of a PCA. + 2nd PC + MS + MS:4000082 + second principal component + + + + + Data from the second principal component of a PCA. + PSI:MS + + + + + + + + + + + + + + + Data from the third principal component of a PCA. + 3rd PC + MS + MS:4000083 + third principal component + + + + + Data from the third principal component of a PCA. + PSI:MS + + + + + + + + + + + + + + + Data from the fourth principal component of a PCA. + 4th PC + MS + MS:4000084 + fourth principal component + + + + + Data from the fourth principal component of a PCA. + PSI:MS + + + + + + + + + + + + + + + Data from the fifth principal component of a PCA. + 5th PC + MS + MS:4000085 + fifth principal component + + + + + Data from the fifth principal component of a PCA. + PSI:MS + + + + + + + + + + + + + + + Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels. + MS + MS:4000086 + mzQC input reference + + + + + Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels. + PSI:MS + + + + + + + + + + + + + + + Used to supply alternative labels for plotting figures. + MS + MS:4000087 + mzQC plot label + + + + + Used to supply alternative labels for plotting figures. + PSI:MS + + + + + + + + + + + + + + + Used to supply batch label information with any string value. + MS + MS:4000088 + batch label + + + + + Used to supply batch label information with any string value. + PSI:MS + + + + + + + + + + + + + + + Used to supply injection sequence information with consecutive whole numbers. + MS + MS:4000089 + injection sequence label + + + + + Used to supply injection sequence information with consecutive whole numbers. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A table with the PCA results of MaxQuant's protein group raw intensities. + MS + MS:4000090 + principal component analysis of MaxQuant's protein group raw intensities + + + + + A table with the PCA results of MaxQuant's protein group raw intensities. + PSI:MS + maxquant:table:directory&s[]=output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A table with the PCA results of MaxQuant's protein group lfq intensities. + MS + MS:4000091 + principal component analysis of MaxQuant's protein group lfq intensities + + + + + A table with the PCA results of MaxQuant's protein group lfq intensities. + PSI:MS + maxquant:table:directory&s[]=output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A table with the PCA results of identified MS1 feature areas. + MS + MS:4000092 + identified MS1 feature area principal component analysis result + + + + + A table with the PCA results of identified MS1 feature areas. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas. + MS + MS:4000093 + unidentified MS1 feature area principal component analysis result + + + + + A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A table with the PCA results of identified MS1 feature areas after batch-correction. + MS + MS:4000094 + batch-corrected identified MS1 feature area principal component analysis result + + + + + A table with the PCA results of identified MS1 feature areas after batch-correction. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. + MS + MS:4000095 + slowest frequency for MS level 1 collection + + + + + The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. + MS + MS:4000096 + slowest frequency for MS level 2 collection + + + + + The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues. + MS + IS-1A + MS:4000097 + MS1 signal jump (10x) count + + + + + The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues. + MS + IS-1B + MS:4000098 + MS1 signal fall (10x) count + + + + + The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). + MS + MS:4000099 + number of empty MS1 scans + + + + + Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). + MS + MS:4000100 + number of empty MS2 scans + + + + + Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). + MS + MS:4000101 + number of empty MS3 scans + + + + + Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of datapoints detected for quantification purposes within the run. These datapoints may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the meta data or analysis methods section of the recording file for the respective run. + MS + MS:4000102 + number of detected quantification data points + + + + + The number of datapoints detected for quantification purposes within the run. These datapoints may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the meta data or analysis methods section of the recording file for the respective run. + PSI:MS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The number of identified datapoints for quantification purposes withing the run after user defined acceptance criteria are applied. These datapoints may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the meta data or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS + MS:4000103 + number of identified quantification data points + + + + + The number of identified datapoints for quantification purposes withing the run after user defined acceptance criteria are applied. These datapoints may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the meta data or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + PSI:MS + + + + + + + + + A practiced and regimented skill or series of actions. + MS + NCIT:C16847 + Technique + + + + + A practiced and regimented skill or series of actions. + NCI + + + + + + + + + A method of analyzing or representing statistical data; a procedure for calculating a statistic. + MS + NCIT:C19044 + Statistical Technique + + + + + A method of analyzing or representing statistical data; a procedure for calculating a statistic. + NCI + + + + + + + + An organizational header for concepts representing mostly abstract entities. + Conceptual Entity + MS + NCIT:C20181 + Conceptual Entity + + + + + An organizational header for concepts representing mostly abstract entities. + NCI + + + + + Conceptual Entity + PT + NCI + + + + + + + + A distinguishing quality or prominent aspect of a person, object, action, process, or substance. + Property or Attribute + MS + NCIT:C20189 + Property or Attribute + + + + + A distinguishing quality or prominent aspect of a person, object, action, process, or substance. + NCI + + + + + Property or Attribute + PT + NCI + + + + + Property or Attribute + PT + NICHD + + + + + + + + + Terms used to indicate units of time or other terms associated with time. + Temporal Qualifier + MS + NCIT:C21514 + Temporal Qualifier + + + + + Terms used to indicate units of time or other terms associated with time. + NCI + + + + + Temporal Qualifier + PT + NCI + + + + + Temporal Qualifier + PT + NICHD + + + + + + + + + The period of time during which something continues. + MS + NCIT:C25330 + Duration + + + + + The period of time during which something continues. + NCI + + + + + + + + + A thing done. + Action + Generic Action + MS + NCIT:C25404 + + Action + + + + + A thing done. + NCI + + + + + Action + PT + NCI + + + + + Action + SY + caDSR + + + + + Generic Action + SY + NCI + + + + + + + + + The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. + Characteristic + Characteristics + Feature + Features + MS + NCIT:C25447 + Characteristic + + + + + The distinguishing qualities or prominent aspect of a person, object, action, process, or substance. + NCI + + + + + Characteristic + PT + NCI + + + + + Characteristic + PT + NICHD + + + + + Characteristic + SY + caDSR + + + + + Characteristics + SY + NCI + + + + + Feature + SY + NCI + + + + + Features + SY + caDSR + + + + + + + + + A term that helps define and render a concept unique. + Modifier + Qualifier + MS + NCIT:C41009 + Qualifier + + + + + A term that helps define and render a concept unique. + NCI + + + + + Modifier + SY + NCI + + + + + Qualifier + PT + NCI + + + + + + + + An active process; excludes processes and mechanisms which fulfill biological functions. + Activity + General activity + MS + NCIT:C43431 + Activity + + + + + An active process; excludes processes and mechanisms which fulfill biological functions. + NCI + + + + + Activity + PT + BRIDG 3.0.3 + + + + + Activity + PT + BRIDG 5.3 + + + + + Activity + PT + NCI + + + + + Activity + SY + caDSR + + + + + General activity + SY + caDSR + + + + + + + + + The amount of something per unit size. + MS + NCIT:C45781 + Density + + + + + The amount of something per unit size. + NCI + + + + + + + + + One of the axes representing the projection of varience resulting from principal component analysis. + MS + NCIT:C60694 + Principal Component + + + + + One of the axes representing the projection of varience resulting from principal component analysis. + NCI + + + + + + + + + Span a region or interval of distance, space or time. + MS + NCIT:C68811 + Cover + + + + + Span a region or interval of distance, space or time. + NCI + + + + + + + + + An observation in a data set that is numerically distant from the rest of the data. + MS + NCIT:C79083 + Outlier + + + + + An observation in a data set that is numerically distant from the rest of the data. + NCI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PSI Extended FASTA Format controlled vocabulary term. + MS + PEFF:0000001 + PEFF CV term + + + + + PSI Extended FASTA Format controlled vocabulary term. + PSI:PEFF + + + + + + + + + CV term that may appear in a PEFF file header section. + MS + PEFF:0000002 + PEFF file header section term + + + + + CV term that may appear in a PEFF file header section. + PSI:PEFF + + + + + + + + + CV term that may appear in a description line of a PEFF file individual sequence entry. + MS + PEFF:0000003 + PEFF file sequence entry term + + + + + CV term that may appear in a description line of a PEFF file individual sequence entry. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the sequence database name. + MS + PEFF:0000008 + DbName + + + + + PEFF keyword for the sequence database name. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the sequence database prefix. + MS + PEFF:0000009 + Prefix + + + + + PEFF keyword for the sequence database prefix. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the sequence database short description. + MS + PEFF:0000010 + DbDescription + + + + + PEFF keyword for the sequence database short description. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the specifying whether the sequence database is a decoy database. + MS + PEFF:0000011 + Decoy + + + + + PEFF keyword for the specifying whether the sequence database is a decoy database. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the source of the database file. + MS + PEFF:0000012 + DbSource + + + + + PEFF keyword for the source of the database file. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the database version (release date) according to database provider. + MS + PEFF:0000013 + DbVersion + + + + + PEFF keyword for the database version (release date) according to database provider. + PSI:PEFF + + + + + + + + + OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider. + MS + PEFF:0000014 + This term was obsoleted. + DbDate + true + + + + + OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the sumber of sequence entries in the database. + MS + PEFF:0000015 + NumberOfEntries + + + + + PEFF keyword for the sumber of sequence entries in the database. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the description of the conversion from original format to this current one. + MS + PEFF:0000016 + Conversion + + + + + PEFF keyword for the description of the conversion from original format to this current one. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for the molecular type of the sequences. + MS + PEFF:0000017 + SequenceType + + + + + PEFF keyword for the molecular type of the sequences. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for database specific keywords not included in the current controlled vocabulary. + MS + PEFF:0000018 + SpecificKey + + + + + PEFF keyword for database specific keywords not included in the current controlled vocabulary. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the specific values for a custom key. + MS + PEFF:0000019 + SpecificValue + + + + + PEFF keyword for the specific values for a custom key. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the short description of the PEFF file. + MS + PEFF:0000020 + DatabaseDescription + + + + + PEFF keyword for the short description of the PEFF file. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for a general comment. + MS + PEFF:0000021 + GeneralComment + + + + + PEFF keyword for a general comment. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms. + MS + PEFF:0000022 + ProteoformDb + + + + + PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location. + MS + PEFF:0000023 + OptionalTagDef + + + + + PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation. + MS + PEFF:0000024 + HasAnnotationIdentifiers + + + + + PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation. + PSI:PEFF + + + + + + + + + + + + + + + OBSOLETE Sequence database unique identifier. + MS + PEFF:0001001 + This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant. + DbUniqueId + true + + + + + OBSOLETE Sequence database unique identifier. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the protein full name. + MS + PEFF:0001002 + PName + + + + + PEFF keyword for the protein full name. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the NCBI taxonomy identifier. + MS + PEFF:0001003 + NcbiTaxId + + + + + PEFF keyword for the NCBI taxonomy identifier. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the taxonomy name (latin or common name). + MS + PEFF:0001004 + TaxName + + + + + PEFF keyword for the taxonomy name (latin or common name). + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the gene name. + MS + PEFF:0001005 + GName + + + + + PEFF keyword for the gene name. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the sequence length. + MS + PEFF:0001006 + Length + + + + + PEFF keyword for the sequence length. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the sequence version. + MS + PEFF:0001007 + SV + + + + + PEFF keyword for the sequence version. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the entry version. + MS + PEFF:0001008 + EV + + + + + PEFF keyword for the entry version. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the Protein Evidence; A UniProtKB code 1-5. + MS + PEFF:0001009 + PE + + + + + PEFF keyword for the Protein Evidence; A UniProtKB code 1-5. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains. + MS + PEFF:0001010 + Processed + + + + + PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + OBSOLETE Sequence variation (substitution, insertion, deletion). + MS + PEFF:0001011 + This term was made obsolete in favor of VariantSimple and VariantComplex. + Variant + true + + + + + OBSOLETE Sequence variation (substitution, insertion, deletion). + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for the modified residue with PSI-MOD identifier. + MS + PEFF:0001012 + ModResPsi + + + + + PEFF keyword for the modified residue with PSI-MOD identifier. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier. + MS + PEFF:0001013 + ModRes + + + + + PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the Alternative Accession Code. + MS + PEFF:0001014 + AltAC + + + + + PEFF keyword for the Alternative Accession Code. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for the sequence status. Complete or Fragment. + MS + PEFF:0001015 + SeqStatus + + + + + PEFF keyword for the sequence status. Complete or Fragment. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the entry associated comment. + MS + PEFF:0001016 + CC + + + + + PEFF keyword for the entry associated comment. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the entry associated keyword(s). + MS + PEFF:0001017 + KW + + + + + PEFF keyword for the entry associated keyword(s). + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the Gene Ontology code. + MS + PEFF:0001018 + GO + + + + + PEFF keyword for the Gene Ontology code. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the cross-reference to an external resource. + MS + PEFF:0001019 + XRef + + + + + PEFF keyword for the cross-reference to an external resource. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed. + MS + PEFF:0001020 + mature protein + + + + + Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein. + MS + PEFF:0001021 + signal peptide + + + + + Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle. + MS + PEFF:0001022 + transit peptide + + + + + Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for the sequence conflict; a UniProtKB term. + MS + PEFF:0001023 + Conflict + + + + + PEFF keyword for the sequence conflict; a UniProtKB term. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the Sequence checksum in crc64. + MS + PEFF:0001024 + Crc64 + + + + + PEFF keyword for the Sequence checksum in crc64. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the sequence range of a domain. + MS + PEFF:0001025 + Domain + + + + + PEFF keyword for the sequence range of a domain. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term. + MS + PEFF:0001026 + ID + + + + + PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for the modified residue with UniMod identifier. + MS + PEFF:0001027 + ModResUnimod + + + + + PEFF keyword for the modified residue with UniMod identifier. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term. + MS + PEFF:0001028 + VariantSimple + + + + + PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon. + MS + PEFF:0001029 + VariantComplex + + + + + PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers. + MS + PEFF:0001030 + Proteoform + + + + + PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications. + MS + PEFF:0001031 + DisulfideBond + + + + + PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications. + PSI:PEFF + + + + + + + + + PEFF keyword describing the type of processing event being described. + MS + PEFF:0001032 + PEFF molecule processing keyword + + + + + PEFF keyword describing the type of processing event being described. + PSI:PEFF + + + + + + + + + + + + + + + PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary. + MS + PEFF:0001033 + Comment + + + + + PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide. + MS + PEFF:0001034 + propeptide + + + + + Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide. + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + N-terminal methionine residue of a protein that can be co-translationally cleaved. + MS + PEFF:0001035 + initiator methionine + + + + + N-terminal methionine residue of a protein that can be co-translationally cleaved. + PSI:PEFF + + + + + + + + + ([0-9]+|[A-Z*](|.+)?). + MS + PEFF:1002001 + regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment + + + + + ([0-9]+|[A-Z*](|.+)?). + PSI:PEFF + + + + + + + + + (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+). + MS + PEFF:1002002 + regular expression for PEFF molecular sequence type + + + + + (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+). + PSI:PEFF + + + + + + + + + (Complete|Fragment|[a-z0-9A-Z]+). + MS + PEFF:1002003 + regular expression for PEFF sequence status + + + + + (Complete|Fragment|[a-z0-9A-Z]+). + PSI:PEFF + + + + + + + + + + + + + + + + + + + + + + + + + + A unit of measurement is a standardized quantity of a physical quality. + george gkoutos + unit.ontology + UO:0000000 + unit + + + + + A unit of measurement is a standardized quantity of a physical quality. + Wikipedia:Wikipedia + + + + + + + + + + + + + + + A unit which is a standard measure of the distance between two points. + george gkoutos + unit.ontology + UO:0000001 + + length unit + + + + + A unit which is a standard measure of the distance between two points. + Wikipedia:Wikipedia + + + + + + + + + + + + + + + + + + + + + A unit which is a standard measure of the amount of matter/energy of a physical object. + george gkoutos + unit.ontology + UO:0000002 + + mass unit + + + + + A unit which is a standard measure of the amount of matter/energy of a physical object. + Wikipedia:Wikipedia + + + + + + + + + + + + + + + + + + + + + A unit which is a standard measure of the dimension in which events occur in sequence. + george gkoutos + UO:0000149 + time derived unit + unit.ontology + UO:0000003 + + time unit + + + + + A unit which is a standard measure of the dimension in which events occur in sequence. + Wikipedia:Wikipedia + + + + + + + + + + + + + + + A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. + george gkoutos + UO:0000126 + temperature derived unit + unit.ontology + UO:0000005 + + temperature unit + + + + + A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. + Wikipedia:Wikipedia + + + + + + + + + + A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. + george gkoutos + m + metre + unit.ontology + UO:0000008 + + meter + + + + + A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. + BIPM:BIPM + NIST:NIST + + + + + + + + + + A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + george gkoutos + s + unit.ontology + UO:0000010 + + second + + + + + A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + BIPM:BIPM + NIST:NIST + + + + + + + + + + A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. + george gkoutos + K + unit.ontology + UO:0000012 + + kelvin + + + + + A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water. + BIPM:BIPM + NIST:NIST + + + + + + + + + A length unit which is equal to one millionth of a meter or 10^[-6] m. + george gkoutos + micrometre + micron + um + unit.ontology + UO:0000017 + + micrometer + + + + + A length unit which is equal to one millionth of a meter or 10^[-6] m. + NIST:NIST + + + + + + + + + A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. + george gkoutos + nanometre + nm + unit.ontology + UO:0000018 + + nanometer + + + + + A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. + NIST:NIST + + + + + + + + + A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. + george gkoutos + g + unit.ontology + UO:0000021 + + gram + + + + + A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. + NIST:NIST + + + + + + + + + A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. + george gkoutos + C + unit.ontology + UO:0000027 + + degree Celsius + + + + + A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. + NIST:NIST + + + + + + + + + A time unit which is equal to one thousandth of a second or 10^[-3] s. + george gkoutos + ms + unit.ontology + UO:0000028 + + millisecond + + + + + A time unit which is equal to one thousandth of a second or 10^[-3] s. + NIST:NIST + + + + + + + + + A time unit which is equal to 60 seconds. + george gkoutos + min + unit.ontology + UO:0000031 + + minute + + + + + A time unit which is equal to 60 seconds. + Wikipedia:Wikipedia + + + + + + + + + A unit which is one of a particular measure to which all measures of that type can be related. + george gkoutos + unit.ontology + UO:0000045 + + base unit + + + + + A unit which is one of a particular measure to which all measures of that type can be related. + NIST:NIST + + + + + + + + + + + + + + + A unit which is a standard measure of the amount of a 2-dimensional flat surface. + george gkoutos + unit.ontology + UO:0000047 + + area unit + + + + + A unit which is a standard measure of the amount of a 2-dimensional flat surface. + UOC:GVG + + + + + + + + + + + + + + + A density unit which is a standard measure of the mass of a substance in a given volume. + george gkoutos + mass per unit volume + unit.ontology + UO:0000052 + + mass density unit + + + + + A density unit which is a standard measure of the mass of a substance in a given volume. + UOC:GVG + + + + + + + + + + + + + + + A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. + george gkoutos + unit.ontology + UO:0000095 + + volume unit + + + + + A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. + NIST:NIST + + + + + + + + + A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. + george gkoutos + millilitre + ml + unit.ontology + UO:0000098 + + milliliter + + + + + A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. + NIST:NIST + + + + + + + + + + + + + + + A unit which is a standard measure of the number of repetitive actions in a particular time. + george gkoutos + unit.ontology + UO:0000105 + + frequency unit + + + + + A unit which is a standard measure of the number of repetitive actions in a particular time. + NIST:NIST + + + + + + + + + A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. + george gkoutos + Hz + s^1 + unit.ontology + UO:0000106 + + hertz + + + + + A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. + NIST:NIST + + + + + + + + + + + + + + + A unit which is a standard measure of the force applied to a given area. + george gkoutos + unit.ontology + UO:0000109 + + pressure unit + + + + + A unit which is a standard measure of the force applied to a given area. + NIST:NIST + + + + + + + + + A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]. + george gkoutos + Pa + unit.ontology + UO:0000110 + + pascal + + + + + A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]. + NIST:NIST + + + + + + + + + + + + + + + + + + + + + A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc). + george gkoutos + unit.ontology + UO:0000111 + + energy unit + + + + + A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc). + NIST:NIST + + + + + + + + + An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force. + george gkoutos + J + unit.ontology + UO:0000112 + + joule + + + + + An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force. + NIST:NIST + + + + + + + + + + + + + + + A unit which is a standard measure of the figure or space formed by the junction of two lines or planes. + george gkoutos + unit.ontology + UO:0000121 + + angle unit + + + + + A unit which is a standard measure of the figure or space formed by the junction of two lines or planes. + Wikipedia:Wikipedia + + + + + + + + + A unit which is a standard measure of the angle formed by two straight lines in the same plane. + george gkoutos + unit.ontology + UO:0000122 + + plane angle unit + + + + + A unit which is a standard measure of the angle formed by two straight lines in the same plane. + Wikipedia:Wikipedia + + + + + + + + + + true + + + + + + + + + + true + + + + + + + + + A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s. + george gkoutos + ns + unit.ontology + UO:0000150 + + nanosecond + + + + + A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s. + NIST:NIST + + + + + + + + + A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance. + george gkoutos + unit.ontology + UO:0000166 + + parts per notation unit + + + + + A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance. + Wikipedia:Wikipedia + + + + + + + + + A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]. + george gkoutos + 10^[-6] + ppm + unit.ontology + UO:0000169 + + parts per million + + + + + A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]. + UOC:GVG + + + + + + + + + A mass unit density which is equal to mass of an object in grams divided by the volume in liters. + george gkoutos + g/L + gram per litre + unit.ontology + UO:0000175 + + gram per liter + + + + + A mass unit density which is equal to mass of an object in grams divided by the volume in liters. + UOC:GVG + + + + + + + + + + + + + + + A unit which is a standard measure of the influence exerted by some mass. + george gkoutos + unit.ontology + UO:0000182 + + density unit + + + + + A unit which is a standard measure of the influence exerted by some mass. + Wikipedia:Wikipedia + + + + + + + + + A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad. + george gkoutos + unit.ontology + UO:0000185 + + degree + + + + + A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad. + Wikipedia:Wikipedia + + + + + + + + + A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. + george gkoutos + unit.ontology + UO:0000186 + + dimensionless unit + + + + + A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. + Wikipedia:Wikipedia + + + + + + + + + A dimensionless ratio unit which denotes numbers as fractions of 100. + george gkoutos + % + unit.ontology + UO:0000187 + + percent + + + + + A dimensionless ratio unit which denotes numbers as fractions of 100. + Wikipedia:Wikipedia + + + + + + + + + A dimensionless unit which denotes a simple count of things. + george gkoutos + count + unit.ontology + UO:0000189 + + count unit + + + + + A dimensionless unit which denotes a simple count of things. + MGED:MGED + + + + + + + + + A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. + george gkoutos + unit.ontology + UO:0000190 + + ratio + + + + + A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. + Wikipedia:Wikipedia + + + + + + + + + A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). + george gkoutos + unit.ontology + UO:0000191 + + fraction + + + + + A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). + Wikipedia:Wikipedia + + + + + + + + + + + + + + + A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field. + george gkoutos + unit.ontology + UO:0000217 + + electric potential difference unit + + + + + A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field. + Wikipedia:Wikipedia + + + + + + + + + An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy. + george gkoutos + V + unit.ontology + UO:0000218 + + volt + + + + + An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy. + Wikipedia:Wikipedia + + + + + + + + + An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state. + george gkoutos + Da + amu + u + unified atomic mass unit + unit.ontology + UO:0000221 + + dalton + + + + + An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state. + Wikipedia:Wikipedia + + + + + + + + + A mass unit which is equal to one thousand daltons. + george gkoutos + kDa + unit.ontology + UO:0000222 + + kilodalton + + + + + A mass unit which is equal to one thousand daltons. + Wikipedia:Wikipedia + + + + + + + + + A unit which is a standard measure of the strength of a magnetic field. + george gkoutos + B + unit.ontology + UO:0000227 + + magnetic flux density unit + + + + + A unit which is a standard measure of the strength of a magnetic field. + allnet:allnet + + + + + + + + + A magnetic flux density unit which is equal to one weber per square meter. + george gkoutos + T + Wb/m2 + unit.ontology + UO:0000228 + + tesla + + + + + A magnetic flux density unit which is equal to one weber per square meter. + WordNet:WordNet + + + + + + + + + A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J. + george gkoutos + eV + electron volt + unit.ontology + UO:0000266 + + electronvolt + + + + + A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J. + Wikipedia:Wikipedia + + + + + + + + + The electric field strength is a unit which is a measure of the potential difference between two points some distance apart. + george gkoutos + 2009-03-03T12:23:16Z + E-field strength + unit.ontology + UO:0000267 + + electric field strength unit + + + + + The electric field strength is a unit which is a measure of the potential difference between two points some distance apart. + Wikipedia:http://en.wikipedia.org/wiki/Electric_field + + + + + + + + + The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart. + george gkoutos + 2009-03-03T12:28:17Z + V/m + volt per metre + unit.ontology + UO:0000268 + + volt per meter + + + + + The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart. + Wikipedia:http://en.wikipedia.org/wiki/Electric_field + + + + + + + + + A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light. + george gkoutos + 2009-07-14T12:33:48Z + AU + unit.ontology + UO:0000269 + + absorbance unit + + + + + A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light. + Wikipedia:http://en.wikipedia.org/wiki/Absorbance + + + + + + + + + A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . + george gkoutos + unit.ontology + UO:0000270 + + volumetric flow rate unit + + + + + A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . + Wikipedia:Wikipedia + + + + + + + + + + + + + + + A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. + george gkoutos + microlitres per minute + uL/min + unit.ontology + UO:0000271 + + microliters per minute + + + + + A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. + UOC:GVG + + + + + + + + + An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long. + gkoutos + 2013-06-27T05:06:40Z + unit.ontology + A^[2] + UO:0000324 + square angstrom + + + + + An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long. + UOC:GVG + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/MassBank-Project/MassBank-lib/src/main/scripts/Msbnk2JSONLD b/MassBank-Project/MassBank-lib/src/main/scripts/Msbnk2JSONLD new file mode 100644 index 00000000..8ee64889 --- /dev/null +++ b/MassBank-Project/MassBank-lib/src/main/scripts/Msbnk2JSONLD @@ -0,0 +1,9 @@ +#!/bin/bash + +JAVA_EXECUTABLE="`which java`" + +DIST_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )/../" && pwd )" +LIB_DIR="$DIST_DIR/lib" + +$JAVA_EXECUTABLE -cp "$LIB_DIR/*" \ +massbank.cli.Msbnk2JSONLD "$@" diff --git a/MassBank-Project/MassBank-lib/src/test/java/massbank/CVUtilTest.java b/MassBank-Project/MassBank-lib/src/test/java/massbank/CVUtilTest.java new file mode 100644 index 00000000..8d3e373e --- /dev/null +++ b/MassBank-Project/MassBank-lib/src/test/java/massbank/CVUtilTest.java @@ -0,0 +1,171 @@ +package massbank; + +import java.io.BufferedReader; +import java.io.ByteArrayInputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.text.ParseException; +import java.util.List; +import java.util.Set; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; + +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.semanticweb.owlapi.model.parameters.Imports.INCLUDED; +import static org.semanticweb.owlapi.search.EntitySearcher.getAnnotationObjects; +import static org.semanticweb.owlapi.search.Searcher.sup; +import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList; +import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asSet; +import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asUnorderedSet; +import static org.semanticweb.owlapi.vocab.OWLFacet.MAX_EXCLUSIVE; +import static org.semanticweb.owlapi.vocab.OWLFacet.MIN_INCLUSIVE; + +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashSet; +import java.util.Iterator; +import java.util.List; +import java.util.Set; + +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.formats.ManchesterSyntaxDocumentFormat; +import org.semanticweb.owlapi.formats.OWLXMLDocumentFormat; +import org.semanticweb.owlapi.formats.TurtleDocumentFormat; +import org.semanticweb.owlapi.io.StreamDocumentTarget; +import org.semanticweb.owlapi.io.StringDocumentSource; +import org.semanticweb.owlapi.io.StringDocumentTarget; +import org.semanticweb.owlapi.model.AddAxiom; +import org.semanticweb.owlapi.model.AddOntologyAnnotation; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLClassExpressionVisitor; +import org.semanticweb.owlapi.model.OWLDataExactCardinality; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDataProperty; +import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLDataPropertyRangeAxiom; +import org.semanticweb.owlapi.model.OWLDataRange; +import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLDataUnionOf; +import org.semanticweb.owlapi.model.OWLDatatype; +import org.semanticweb.owlapi.model.OWLDatatypeDefinitionAxiom; +import org.semanticweb.owlapi.model.OWLDatatypeRestriction; +import org.semanticweb.owlapi.model.OWLDeclarationAxiom; +import org.semanticweb.owlapi.model.OWLDifferentIndividualsAxiom; +import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom; +import org.semanticweb.owlapi.model.OWLDocumentFormat; +import org.semanticweb.owlapi.model.OWLEntity; +import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom; +import org.semanticweb.owlapi.model.OWLFacetRestriction; +import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom; +import org.semanticweb.owlapi.model.OWLIndividual; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedIndividual; +import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom; +import org.semanticweb.owlapi.model.OWLObjectExactCardinality; +import org.semanticweb.owlapi.model.OWLObjectHasValue; +import org.semanticweb.owlapi.model.OWLObjectIntersectionOf; +import org.semanticweb.owlapi.model.OWLObjectOneOf; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyID; +import org.semanticweb.owlapi.model.OWLOntologyIRIMapper; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; +import org.semanticweb.owlapi.model.OWLSubClassOfAxiom; +import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom; +import org.semanticweb.owlapi.model.PrefixManager; +import org.semanticweb.owlapi.model.SWRLAtom; +import org.semanticweb.owlapi.model.SWRLObjectPropertyAtom; +import org.semanticweb.owlapi.model.SWRLRule; +import org.semanticweb.owlapi.model.SWRLVariable; +import org.semanticweb.owlapi.model.SetOntologyID; +import org.semanticweb.owlapi.reasoner.BufferingMode; +import org.semanticweb.owlapi.reasoner.InferenceType; +import org.semanticweb.owlapi.reasoner.Node; +import org.semanticweb.owlapi.reasoner.NodeSet; +import org.semanticweb.owlapi.reasoner.OWLReasoner; +import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; +import org.semanticweb.owlapi.reasoner.SimpleConfiguration; +import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner; +import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory; +import org.semanticweb.owlapi.search.Filters; +import org.semanticweb.owlapi.util.AutoIRIMapper; +import org.semanticweb.owlapi.util.DefaultPrefixManager; +import org.semanticweb.owlapi.util.InferredAxiomGenerator; +import org.semanticweb.owlapi.util.InferredOntologyGenerator; +import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator; +import org.semanticweb.owlapi.util.OWLEntityRemover; +import org.semanticweb.owlapi.util.OWLOntologyMerger; +import org.semanticweb.owlapi.util.OWLOntologyWalker; +import org.semanticweb.owlapi.util.OWLOntologyWalkerVisitorEx; +import org.semanticweb.owlapi.util.SimpleIRIMapper; +import org.semanticweb.owlapi.vocab.OWL2Datatype; +import org.semanticweb.owlapi.vocab.OWLFacet; + +import uk.ac.manchester.cs.owlapi.modularity.ModuleType; +import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor; + +public class CVUtilTest { + +//private OboParser parser; + + //@Test +// public void testCVUtilGetFirst() { +// CVUtil cvUtil = CVUtil.get(); +// Assertions.assertTrue(cvUtil.ontology.containsTerm("MS:0000000")); +// Assertions.assertFalse(cvUtil.ontology.containsTerm("MS:2000000")); +// } +// +// //@Test +// public void testCVUtilGetSecond() { +// CVUtil cvUtil = CVUtil.get(); +// Assertions.assertTrue(cvUtil.ontology.containsTerm("MS:0000000")); +// Assertions.assertFalse(cvUtil.ontology.containsTerm("MS:2000000")); +// } + + @Test + public void testTermIsA() throws IOException, OWLOntologyStorageException, OWLOntologyCreationException { + CVUtil cvUtil = CVUtil.get(); + Assertions.assertTrue(cvUtil.termIsA("MS:1003294","MS:1000250")); +// IOHelper ioHelper = new IOHelper(); +// OWLOntology full = ioHelper.loadOntology("/home/rene/GIT/MassBank-web/MassBank-Project/MassBank-lib/src/main/resources/cv/psi-ms.owl"); +// +// +// OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); +// OWLOntology ontology = manager.loadOntology(IRI.create("https://protege.stanford.edu/ontologies/pizza/pizza.owl")); +// ontology.saveOntology(new FunctionalSyntaxDocumentFormat(), System.out); +// +// OWLOntologyManager man = OWLManager.createOWLOntologyManager(); +// System.out.println(man.getOntologies().size()); + + } + + + +} \ No newline at end of file diff --git a/MassBank-Project/MassBank-lib/src/test/java/massbank/RecordParserDefinitionTest.java b/MassBank-Project/MassBank-lib/src/test/java/massbank/RecordParserDefinitionTest.java index f200d563..fd0a9056 100644 --- a/MassBank-Project/MassBank-lib/src/test/java/massbank/RecordParserDefinitionTest.java +++ b/MassBank-Project/MassBank-lib/src/test/java/massbank/RecordParserDefinitionTest.java @@ -28,8 +28,22 @@ private Result assertInvalid(String source, String production) { @Test public void testACCESSION() { - assertValid("ACCESSION: MSBNK-Aa10_zZ-Aa10_zZ\n", "accession"); - assertInvalid("ACCESSION: MSBNK-Aa:10_zZ-Aa10_zZ\n", "accession"); + assertValid("ACCESSION: MSBNK-Aa10_zZ-A10_Z\n", "accession"); + assertInvalid("ACCESSION: MSBNK-Aa:10_zZ-A10_Z\n", "accession"); + } + + @Test + public void testCVterm() { + assertValid("[MS,,,]", "cvterm"); + assertValid("[MS ,,,]", "cvterm"); + assertValid("[ MS ,,,]", "cvterm"); + assertValid("[,,,]", "cvterm"); + assertValid("[ ,,,]", "cvterm"); + assertValid("[MS, MS:1001477, SpectraST,]", "cvterm"); + assertValid("[MOD, MOD:00648, \"N,O-diacetylated L-serine\",]", "cvterm"); + assertValid("[MS, MS:1003294, electron activated dissociation,]", "cvterm_validated"); +// assertInvalid("[MS, MMMS:1003294, electron activated dissociation,]", "cvterm_validated"); +// assertInvalid("[MS, MS:1003294, collision-induced dissociation,]", "cvterm_validated"); } } diff --git a/MassBank-Project/MassBank-lib/src/test/java/massbank/export/RecordToJsonTest.java b/MassBank-Project/MassBank-lib/src/test/java/massbank/export/RecordToJsonTest.java index c8f007f3..5cac64de 100644 --- a/MassBank-Project/MassBank-lib/src/test/java/massbank/export/RecordToJsonTest.java +++ b/MassBank-Project/MassBank-lib/src/test/java/massbank/export/RecordToJsonTest.java @@ -17,31 +17,51 @@ public class RecordToJsonTest { @Test - public void testToJson() throws IOException, URISyntaxException { + public void testToJsonMinimalRecord() throws IOException, URISyntaxException { String minimalRecordString = Files - .readString(Paths.get(getClass().getClassLoader().getResource("minimal_record.txt").toURI())); + .readString(Paths.get(getClass().getClassLoader().getResource("MSBNK-test-TST00001.txt").toURI())); String minimalJson = Files .readString(Paths.get(getClass().getClassLoader().getResource("minimal_record.json").toURI())); Record minimalRecord = Validator.validate(minimalRecordString, new HashSet()); String minimalRecordJson = RecordToJson.convert(minimalRecord); Assertions.assertEquals(minimalJson, minimalRecordJson); - + } + + @Test + public void testToJsonMaximalRecord() throws IOException, URISyntaxException { String maximalRecordString = Files - .readString(Paths.get(getClass().getClassLoader().getResource("maximal_record.txt").toURI())); + .readString(Paths.get(getClass().getClassLoader().getResource("MSBNK-test-TST00002.txt").toURI())); String maximalJson = Files .readString(Paths.get(getClass().getClassLoader().getResource("maximal_record.json").toURI())); Record maximalRecord = Validator.validate(maximalRecordString, new HashSet()); String maximalRecordJson = RecordToJson.convert(maximalRecord); Assertions.assertEquals(maximalJson, maximalRecordJson); + } + @Test + public void testToJsonDeprecatedRecord() throws IOException, URISyntaxException { String deprecatedRecordString = Files - .readString(Paths.get(getClass().getClassLoader().getResource("deprecated_record.txt").toURI())); + .readString(Paths.get(getClass().getClassLoader().getResource("MSBNK-test-TST00003.txt").toURI())); String deprecatedJson = Files .readString(Paths.get(getClass().getClassLoader().getResource("deprecated_record.json").toURI())); Record deprecatedRecord = Validator.validate(deprecatedRecordString, new HashSet()); String deprecatedRecordJson = RecordToJson.convert(deprecatedRecord); Assertions.assertEquals(deprecatedJson, deprecatedRecordJson); + } + + @Test + public void testToJsonCombinedRecord() throws IOException, URISyntaxException { + String minimalRecordString = Files + .readString(Paths.get(getClass().getClassLoader().getResource("MSBNK-test-TST00001.txt").toURI())); + Record minimalRecord = Validator.validate(minimalRecordString, new HashSet()); + String maximalRecordString = Files + .readString(Paths.get(getClass().getClassLoader().getResource("MSBNK-test-TST00002.txt").toURI())); + Record maximalRecord = Validator.validate(maximalRecordString, new HashSet()); + String deprecatedRecordString = Files + .readString(Paths.get(getClass().getClassLoader().getResource("MSBNK-test-TST00003.txt").toURI())); + Record deprecatedRecord = Validator.validate(deprecatedRecordString, new HashSet()); + String combinedJson = Files .readString(Paths.get(getClass().getClassLoader().getResource("combined_record.json").toURI())); List records = new ArrayList(); diff --git a/MassBank-Project/MassBank-lib/src/test/resources/minimal_record.txt b/MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00001.txt similarity index 96% rename from MassBank-Project/MassBank-lib/src/test/resources/minimal_record.txt rename to MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00001.txt index bb510a1c..cbe83175 100644 --- a/MassBank-Project/MassBank-lib/src/test/resources/minimal_record.txt +++ b/MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00001.txt @@ -1,4 +1,4 @@ -ACCESSION: MSBNK-test-tst00001 +ACCESSION: MSBNK-test-TST00001 RECORD_TITLE: Fiscalin C; LC-ESI-ITFT; MS2; CE: 30; R=17500; [M+H]+ DATE: 2017.07.07 AUTHORS: Megan J. Kelman, Justin B. Renaud, Mark W. Sumarah, Agriculture and Agri-Food Canada diff --git a/MassBank-Project/MassBank-lib/src/test/resources/maximal_record.txt b/MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00002.txt similarity index 95% rename from MassBank-Project/MassBank-lib/src/test/resources/maximal_record.txt rename to MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00002.txt index 9d74ebe0..1607ba3f 100644 --- a/MassBank-Project/MassBank-lib/src/test/resources/maximal_record.txt +++ b/MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00002.txt @@ -1,4 +1,4 @@ -ACCESSION: MSBNK-test-tst00002 +ACCESSION: MSBNK-test-TST00002 RECORD_TITLE: Disialoganglioside GD1a; MALDI-TOF; MS; Pos DATE: 2016.01.19 (Created 2009.11.24, modified 2011.05.11) AUTHORS: Wada Y, Osaka Medical Center for Maternal and Child Health @@ -29,6 +29,10 @@ AC$MASS_SPECTROMETRY: ION_MODE POSITIVE AC$MASS_SPECTROMETRY: LASER UV 337 nm nitrogen lazer, 20 Hz, 10 nsec AC$MASS_SPECTROMETRY: MATRIX DHB AC$MASS_SPECTROMETRY: SAMPLE_DRIPPING 500 pmol +AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE [MS, MS:1003294, electron activated dissociation, ] +AC$MASS_SPECTROMETRY: KINETIC_ENERGY 15 eV +AC$MASS_SPECTROMETRY: ELECTRON_CURRENT 6500 nA +AC$MASS_SPECTROMETRY: REACTION_TIME 65 ms AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um, 2.1x100mm, Thermo AC$CHROMATOGRAPHY: FLOW_GRADIENT 99/1 at 0-1 min, 61/39 at 3 min, 0.1/99.9 at 14-16 min, 99/1 at 16.1-20 min AC$CHROMATOGRAPHY: FLOW_RATE 200 uL/min at 0-3 min, 400 uL/min at 14 min, 480 uL/min at 16-19 min, 200 uL/min at 19.1-20 min diff --git a/MassBank-Project/MassBank-lib/src/test/resources/deprecated_record.txt b/MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00003.txt similarity index 98% rename from MassBank-Project/MassBank-lib/src/test/resources/deprecated_record.txt rename to MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00003.txt index 0a775a80..d345dfbd 100644 --- a/MassBank-Project/MassBank-lib/src/test/resources/deprecated_record.txt +++ b/MassBank-Project/MassBank-lib/src/test/resources/MSBNK-test-TST00003.txt @@ -1,4 +1,4 @@ -ACCESSION: MSBNK-test-tst00003 +ACCESSION: MSBNK-test-TST00003 DEPRECATED: 2019-11-25 Wrong MS measurement assigned RECORD_TITLE: 11-HDoHE; LC-ESI-QTOF; MS2; CE: 20.0; R=N/A; [M-H]- DATE: 2018.11.21 diff --git a/MassBank-Project/MassBank-lib/src/test/resources/combined_record.json b/MassBank-Project/MassBank-lib/src/test/resources/combined_record.json index b23dc3fa..22b188c1 100644 --- a/MassBank-Project/MassBank-lib/src/test/resources/combined_record.json +++ b/MassBank-Project/MassBank-lib/src/test/resources/combined_record.json @@ -1,6 +1,6 @@ [ { - "ACCESSION": "MSBNK-test-tst00001", + "ACCESSION": "MSBNK-test-TST00001", "RECORD_TITLE": [ "Fiscalin C", "LC-ESI-ITFT", @@ -45,7 +45,7 @@ ] }, { - "ACCESSION": "MSBNK-test-tst00002", + "ACCESSION": "MSBNK-test-TST00002", "RECORD_TITLE": [ "Disialoganglioside GD1a", "MALDI-TOF", @@ -95,7 +95,11 @@ "AC$MASS_SPECTROMETRY": { "LASER": "UV 337 nm nitrogen lazer, 20 Hz, 10 nsec", "MATRIX": "DHB", - "SAMPLE_DRIPPING": "500 pmol" + "SAMPLE_DRIPPING": "500 pmol", + "FRAGMENTATION_MODE": "[MS, MS:1003294, electron activated dissociation, ]", + "KINETIC_ENERGY": "15 eV", + "ELECTRON_CURRENT": "6500 nA", + "REACTION_TIME": "65 ms" }, "AC$CHROMATOGRAPHY": { "COLUMN_NAME": "Acclaim RSLC C18 2.2um, 2.1x100mm, Thermo", @@ -601,7 +605,7 @@ ] }, { - "ACCESSION": "MSBNK-test-tst00003", + "ACCESSION": "MSBNK-test-TST00003", "DEPRECATED": true, "DEPRECATED_CONTENT": "2019-11-25 Wrong MS measurement assigned\nRECORD_TITLE: 11-HDoHE; LC-ESI-QTOF; MS2; CE: 20.0; R\u003dN/A; [M-H]-\nDATE: 2018.11.21\nAUTHORS: Nils Hoffmann, Dominik Kopczynski, Bing Peng\nLICENSE: CC BY-SA\nCOPYRIGHT: Copyright (C) 2019, Leibniz Institut fuer Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany\nCOMMENT: CONFIDENCE standard compound\nCOMMENT: NATIVE_RUN_ID QExHF03_NM_0001275.mzML\nCOMMENT: PROCESSING averaging of repeated ion fragments at 20.0 eV within 5 ppm window [MS, MS:1000575, mean of spectra, ]\nCH$NAME: 11-HDoHE\nCH$COMPOUND_CLASS: Natural Product; Lipid Standard\nCH$FORMULA: C22H32O3\nCH$EXACT_MASS: 344.23514\nCH$SMILES: CC\\C\u003dC/C\\C\u003dC/C\\C\u003dC/CC(O)\\C\u003dC\\C\u003dC/C\\C\u003dC/CCC(O)\u003dO\nCH$IUPAC: InChI\u003d1S/C22H32O3/c1-2-3-4-5-6-7-9-12-15-18-21(23)19-16-13-10-8-11-14-17-20-22(24)25/h3-4,6-7,10-16,19,21,23H,2,5,8-9,17-18,20H2,1H3,(H,24,25)/b4-3-,7-6-,13-10-,14-11-,15-12-,19-16+\nCH$LINK: CHEBI CHEBI:72794\nCH$LINK: LIPIDMAPS LMFA04000028\nCH$LINK: INCHIKEY LTERDCBCHFKFRI-BGKMTWLOSA-N\nCH$LINK: PUBCHEM CID:11631564\nAC$INSTRUMENT: Q-Exactive HF, Thermo Scientific [MS:1002523]\nAC$INSTRUMENT_TYPE: LC-ESI-QTOF\nAC$MASS_SPECTROMETRY: MS_TYPE MS2\nAC$MASS_SPECTROMETRY: ION_MODE NEGATIVE\nAC$MASS_SPECTROMETRY: IONIZATION ESI\nAC$MASS_SPECTROMETRY: FRAGMENTATION_MODE HCD\nAC$MASS_SPECTROMETRY: COLLISION_ENERGY 20.0 eV\nAC$MASS_SPECTROMETRY: RESOLUTION N/A\nMS$FOCUSED_ION: BASE_PEAK 343.2279\nMS$FOCUSED_ION: PRECURSOR_M/Z 343.2279\nMS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-\nPK$SPLASH: splash10-00dl-0914000000-bad728fe323f6890656d\nPK$ANNOTATION: m/z annotation exact_mass error(ppm)\n 59.013471921284996 59.013 59.0133 2.913263365927882\n 95.0502389272054 95.050 95.0502 0.40954364535633475\n 121.1022351582845 121.102 121.1022 0.29031912309532387\n 149.13346735636392 149.133 149.1333 1.1221931248150303\n 165.09201685587564 165.092 165.0919 0.7078231920609128\n 194.09474436442056 194.095 194.0946 0.7437838072718687\n 281.22726186116535 281.227 281.2273 -0.1356156911126373\n 299.2378336588542 299.238 299.2378 0.1124819597449277\n 325.2170130411784 325.217 325.2171 -0.2673869905083813\n 343.22746022542316 precursor 343.227868554909 -1.1896746249719279\nPK$NUM_PEAK: 10\nPK$PEAK: m/z int. rel.int.\n 59.013471921284996 47825.663583333335 22\n 95.0502389272054 123675.15916666668 58\n 121.1022351582845 2119825.3000000003 999\n 149.13346735636392 538442.9091666666 254\n 165.09201685587564 717615.9775 338\n 194.09474436442056 348560.26666666666 164\n 281.22726186116535 577177.7541666667 271\n 299.2378336588542 162688.84041666667 76\n 325.2170130411784 246360.69083333333 115\n 343.22746022542316 1749842.5083333335 824\n//\n" } diff --git a/MassBank-Project/MassBank-lib/src/test/resources/deprecated_record.json b/MassBank-Project/MassBank-lib/src/test/resources/deprecated_record.json index 1492275d..8b01d29d 100644 --- a/MassBank-Project/MassBank-lib/src/test/resources/deprecated_record.json +++ b/MassBank-Project/MassBank-lib/src/test/resources/deprecated_record.json @@ -1,5 +1,5 @@ { - "ACCESSION": "MSBNK-test-tst00003", + "ACCESSION": "MSBNK-test-TST00003", "DEPRECATED": true, "DEPRECATED_CONTENT": "2019-11-25 Wrong MS measurement assigned\nRECORD_TITLE: 11-HDoHE; LC-ESI-QTOF; MS2; CE: 20.0; R\u003dN/A; [M-H]-\nDATE: 2018.11.21\nAUTHORS: Nils Hoffmann, Dominik Kopczynski, Bing Peng\nLICENSE: CC BY-SA\nCOPYRIGHT: Copyright (C) 2019, Leibniz Institut fuer Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany\nCOMMENT: CONFIDENCE standard compound\nCOMMENT: NATIVE_RUN_ID QExHF03_NM_0001275.mzML\nCOMMENT: PROCESSING averaging of repeated ion fragments at 20.0 eV within 5 ppm window [MS, MS:1000575, mean of spectra, ]\nCH$NAME: 11-HDoHE\nCH$COMPOUND_CLASS: Natural Product; Lipid Standard\nCH$FORMULA: C22H32O3\nCH$EXACT_MASS: 344.23514\nCH$SMILES: CC\\C\u003dC/C\\C\u003dC/C\\C\u003dC/CC(O)\\C\u003dC\\C\u003dC/C\\C\u003dC/CCC(O)\u003dO\nCH$IUPAC: InChI\u003d1S/C22H32O3/c1-2-3-4-5-6-7-9-12-15-18-21(23)19-16-13-10-8-11-14-17-20-22(24)25/h3-4,6-7,10-16,19,21,23H,2,5,8-9,17-18,20H2,1H3,(H,24,25)/b4-3-,7-6-,13-10-,14-11-,15-12-,19-16+\nCH$LINK: CHEBI CHEBI:72794\nCH$LINK: LIPIDMAPS LMFA04000028\nCH$LINK: INCHIKEY LTERDCBCHFKFRI-BGKMTWLOSA-N\nCH$LINK: PUBCHEM CID:11631564\nAC$INSTRUMENT: Q-Exactive HF, Thermo Scientific [MS:1002523]\nAC$INSTRUMENT_TYPE: LC-ESI-QTOF\nAC$MASS_SPECTROMETRY: MS_TYPE MS2\nAC$MASS_SPECTROMETRY: ION_MODE NEGATIVE\nAC$MASS_SPECTROMETRY: IONIZATION ESI\nAC$MASS_SPECTROMETRY: FRAGMENTATION_MODE HCD\nAC$MASS_SPECTROMETRY: COLLISION_ENERGY 20.0 eV\nAC$MASS_SPECTROMETRY: RESOLUTION N/A\nMS$FOCUSED_ION: BASE_PEAK 343.2279\nMS$FOCUSED_ION: PRECURSOR_M/Z 343.2279\nMS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-\nPK$SPLASH: splash10-00dl-0914000000-bad728fe323f6890656d\nPK$ANNOTATION: m/z annotation exact_mass error(ppm)\n 59.013471921284996 59.013 59.0133 2.913263365927882\n 95.0502389272054 95.050 95.0502 0.40954364535633475\n 121.1022351582845 121.102 121.1022 0.29031912309532387\n 149.13346735636392 149.133 149.1333 1.1221931248150303\n 165.09201685587564 165.092 165.0919 0.7078231920609128\n 194.09474436442056 194.095 194.0946 0.7437838072718687\n 281.22726186116535 281.227 281.2273 -0.1356156911126373\n 299.2378336588542 299.238 299.2378 0.1124819597449277\n 325.2170130411784 325.217 325.2171 -0.2673869905083813\n 343.22746022542316 precursor 343.227868554909 -1.1896746249719279\nPK$NUM_PEAK: 10\nPK$PEAK: m/z int. rel.int.\n 59.013471921284996 47825.663583333335 22\n 95.0502389272054 123675.15916666668 58\n 121.1022351582845 2119825.3000000003 999\n 149.13346735636392 538442.9091666666 254\n 165.09201685587564 717615.9775 338\n 194.09474436442056 348560.26666666666 164\n 281.22726186116535 577177.7541666667 271\n 299.2378336588542 162688.84041666667 76\n 325.2170130411784 246360.69083333333 115\n 343.22746022542316 1749842.5083333335 824\n//\n" } \ No newline at end of file diff --git a/MassBank-Project/MassBank-lib/src/test/resources/maximal_record.json b/MassBank-Project/MassBank-lib/src/test/resources/maximal_record.json index bf428320..2134de9d 100644 --- a/MassBank-Project/MassBank-lib/src/test/resources/maximal_record.json +++ b/MassBank-Project/MassBank-lib/src/test/resources/maximal_record.json @@ -1,5 +1,5 @@ { - "ACCESSION": "MSBNK-test-tst00002", + "ACCESSION": "MSBNK-test-TST00002", "RECORD_TITLE": [ "Disialoganglioside GD1a", "MALDI-TOF", @@ -49,7 +49,11 @@ "AC$MASS_SPECTROMETRY": { "LASER": "UV 337 nm nitrogen lazer, 20 Hz, 10 nsec", "MATRIX": "DHB", - "SAMPLE_DRIPPING": "500 pmol" + "SAMPLE_DRIPPING": "500 pmol", + "FRAGMENTATION_MODE": "[MS, MS:1003294, electron activated dissociation, ]", + "KINETIC_ENERGY": "15 eV", + "ELECTRON_CURRENT": "6500 nA", + "REACTION_TIME": "65 ms" }, "AC$CHROMATOGRAPHY": { "COLUMN_NAME": "Acclaim RSLC C18 2.2um, 2.1x100mm, Thermo", diff --git a/MassBank-Project/MassBank-lib/src/test/resources/minimal_record.json b/MassBank-Project/MassBank-lib/src/test/resources/minimal_record.json index a6ddb5a2..5c1c954b 100644 --- a/MassBank-Project/MassBank-lib/src/test/resources/minimal_record.json +++ b/MassBank-Project/MassBank-lib/src/test/resources/minimal_record.json @@ -1,5 +1,5 @@ { - "ACCESSION": "MSBNK-test-tst00001", + "ACCESSION": "MSBNK-test-TST00001", "RECORD_TITLE": [ "Fiscalin C", "LC-ESI-ITFT", diff --git a/MassBank-Project/MassBank-web/pom.xml b/MassBank-Project/MassBank-web/pom.xml index 10578cc2..ab34490c 100644 --- a/MassBank-Project/MassBank-web/pom.xml +++ b/MassBank-Project/MassBank-web/pom.xml @@ -3,7 +3,7 @@ MassBank-Project de.ipb-halle.msbi - 2.2 + 2.2.2 MassBank-web diff --git a/MassBank-Project/MassBank-web/src/main/java/massbank/Contents.java b/MassBank-Project/MassBank-web/src/main/java/massbank/Contents.java index 188cc70c..03ff3aa5 100644 --- a/MassBank-Project/MassBank-web/src/main/java/massbank/Contents.java +++ b/MassBank-Project/MassBank-web/src/main/java/massbank/Contents.java @@ -190,11 +190,8 @@ public void init() throws ServletException { @Override protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { // Preprocess request: load list of mass spectrometry information in JSP. - try { - if (timestamp.isOutdated()) init(); - } catch (SQLException | ConfigurationException e) { - logger.error(e.getMessage()); - } + + if (timestamp.isOutdated()) init(); try { request.setAttribute("sites", result.mapSiteToRecordCount); diff --git a/MassBank-Project/MassBank-web/src/main/java/massbank/RecordDisplay.java b/MassBank-Project/MassBank-web/src/main/java/massbank/RecordDisplay.java index 5970d9e9..ea52fd3f 100644 --- a/MassBank-Project/MassBank-web/src/main/java/massbank/RecordDisplay.java +++ b/MassBank-Project/MassBank-web/src/main/java/massbank/RecordDisplay.java @@ -36,7 +36,6 @@ import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; -import org.apache.commons.lang3.tuple.Pair; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.openscience.cdk.depict.Depiction; diff --git a/MassBank-Project/MassBank-web/src/main/java/massbank/SiteMapServlet.java b/MassBank-Project/MassBank-web/src/main/java/massbank/SiteMapServlet.java index 5e672ffe..bea09ccd 100644 --- a/MassBank-Project/MassBank-web/src/main/java/massbank/SiteMapServlet.java +++ b/MassBank-Project/MassBank-web/src/main/java/massbank/SiteMapServlet.java @@ -22,12 +22,19 @@ import java.io.File; import java.io.IOException; +import java.io.InputStream; import java.net.MalformedURLException; import java.nio.file.Files; import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.SQLException; +import java.time.Instant; +import java.time.ZonedDateTime; +import java.time.format.DateTimeFormatter; +import java.time.temporal.ChronoUnit; +import java.util.Date; import java.util.List; +import java.util.Properties; import javax.servlet.ServletContext; import javax.servlet.ServletException; @@ -42,9 +49,11 @@ import com.redfin.sitemapgenerator.SitemapIndexGenerator; import com.redfin.sitemapgenerator.WebSitemapGenerator; +import com.redfin.sitemapgenerator.WebSitemapUrl; import massbank.db.DatabaseManager; import massbank.db.DatabaseTimestamp; +import massbank.repository.RepositoryInterface; /** * @@ -72,6 +81,25 @@ public void init() throws ServletException { file.delete(); } } + + Properties properties = new Properties(); + try { + InputStream inStream = RepositoryInterface.class.getResourceAsStream("/project.properties"); + if (inStream == null) { + logger.error("Error finding project.properties. File will be ignored."); + properties.setProperty("version", "N/A"); + properties.setProperty("timestamp", Instant.now().truncatedTo(ChronoUnit.SECONDS).toString()); + } else { + properties.load(inStream); + } + } catch (IOException e) { + logger.error("Error reading project.properties. File will be ignored.\n", e); + properties.setProperty("version", "N/A"); + properties.setProperty("timestamp", Instant.now().truncatedTo(ChronoUnit.SECONDS).toString()); + } + + Instant softwareTimestamp = ZonedDateTime.parse(properties.getProperty("timestamp"), DateTimeFormatter.ISO_OFFSET_DATE_TIME).toInstant(); + timestamp = new DatabaseTimestamp(); try { // create sitemap generator @@ -80,17 +108,19 @@ public void init() throws ServletException { WebSitemapGenerator wsg = new WebSitemapGenerator(sitemapbaseurl, tmpdir); // add static content - wsg.addUrl(sitemapbaseurl); - wsg.addUrl(sitemapbaseurl + "Index"); - wsg.addUrl(sitemapbaseurl + "Search"); - wsg.addUrl(sitemapbaseurl + "RecordIndex"); + wsg.addUrl(new WebSitemapUrl.Options(sitemapbaseurl + "Index").lastMod(Date.from(softwareTimestamp)).build()); + wsg.addUrl(new WebSitemapUrl.Options(sitemapbaseurl + "Search").lastMod(Date.from(softwareTimestamp)).build()); + wsg.addUrl(new WebSitemapUrl.Options(sitemapbaseurl + "RecordIndex").lastMod(Date.from(softwareTimestamp)).build()); // add dynamic content DatabaseManager databaseManager= new DatabaseManager("MassBank"); - PreparedStatement stmnt = databaseManager.getConnection().prepareStatement("SELECT ACCESSION FROM RECORD"); + PreparedStatement stmnt = databaseManager.getConnection().prepareStatement("SELECT ACCESSION,RECORD_TIMESTAMP FROM RECORD"); ResultSet res = stmnt.executeQuery(); while (res.next()) { - wsg.addUrl(sitemapbaseurl + "RecordDisplay?id=" + res.getString(1)); + String accession = res.getString(1); + Date recordTimestamp = res.getTimestamp(2); + recordTimestamp = recordTimestamp.before(Date.from(softwareTimestamp)) ? Date.from(softwareTimestamp) : recordTimestamp; + wsg.addUrl(new WebSitemapUrl.Options(sitemapbaseurl + "RecordDisplay?id=" + accession).lastMod(recordTimestamp).build()); } databaseManager.closeConnection(); @@ -104,9 +134,6 @@ public void init() throws ServletException { sig.addUrl(sitemapbaseurl + "sitemap/" + sitemap.getName()); } sig.write(); - - // get the current database timestamp - timestamp=new DatabaseTimestamp(); } catch (ConfigurationException | MalformedURLException | SQLException e) { logger.error(e.getMessage()); } @@ -117,12 +144,8 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re logger.trace("getServletPath: " + request.getServletPath()); logger.trace("getRequestURI: " + request.getRequestURI() ); - try { - if (timestamp.isOutdated()) init(); - } catch (SQLException | ConfigurationException e) { - logger.error(e.getMessage()); - } - + if (timestamp.isOutdated()) init(); + File sitemap; if ((request.getPathInfo() == null) && "/sitemapindex.xml".equals(request.getServletPath())) { sitemap=new File((File)getServletContext().getAttribute(ServletContext.TEMPDIR), request.getServletPath()); diff --git a/MassBank-Project/MassBank-web/src/main/webapp/Contents.jsp b/MassBank-Project/MassBank-web/src/main/webapp/Contents.jsp index 41bf6081..a3e0b9e4 100644 --- a/MassBank-Project/MassBank-web/src/main/webapp/Contents.jsp +++ b/MassBank-Project/MassBank-web/src/main/webapp/Contents.jsp @@ -221,7 +221,7 @@
-
+
Horai, Arita, Kanaya, Nihei, Ikeda, Suwa, Ojima, Tanaka, Tanaka, Aoshima, Oda, Kakazu, Kusano, Tohge, Matsuda, Sawada, Hirai, Nakanishi, Ikeda, Akimoto, Maoka, Takahashi, Ara, Sakurai, Suzuki, Shibata, Neumann, Iida, Tanaka, Funatsu, Matsuura, Soga, Taguchi, Saito, Nishioka. MassBank: a public repository for sharing mass spectral data for life sciences. Journal of mass spectrometry. 2010 Jul;45(7):703-14. doi: 10.1002/jms.1777.
MassBank: a public repository for sharing mass spectral data for life sciences.
diff --git a/MassBank-Project/MassBank-web/src/main/webapp/RecordDisplay.jsp b/MassBank-Project/MassBank-web/src/main/webapp/RecordDisplay.jsp index 4d82da28..31f6ef86 100755 --- a/MassBank-Project/MassBank-web/src/main/webapp/RecordDisplay.jsp +++ b/MassBank-Project/MassBank-web/src/main/webapp/RecordDisplay.jsp @@ -47,8 +47,10 @@ - + + diff --git a/MassBank-Project/pom.xml b/MassBank-Project/pom.xml index ce1c4415..370c7474 100644 --- a/MassBank-Project/pom.xml +++ b/MassBank-Project/pom.xml @@ -1,8 +1,10 @@ - + 4.0.0 de.ipb-halle.msbi MassBank-Project - 2.2 + 2.2.2 MassBank-Project https://github.com/MassBank/MassBank-web pom @@ -28,15 +30,18 @@ UTF-8 ${project.version} - 2.7.1 - 2.7.5 + 2.8 + 2.7.7 2.3.1 2.35 2.13.2 9.4.24.v20191120 1.2.8 1.7.36 - 5.8.2 + 5.9.2 + 2.7.7 + 6.1.0 + 2023-02-02T09:30:31+01:00 @@ -50,7 +55,7 @@ org.apache.logging.log4j log4j-core - 2.17.2 + 2.19.0 jakarta.platform @@ -75,7 +80,7 @@ org.apache.commons commons-configuration2 - 2.7 + 2.8.0 commons-cli @@ -121,34 +126,34 @@ org.json json - 20220320 + 20220924 com.google.code.gson gson - 2.9.0 + 2.10.1 org.apache.httpcomponents httpclient - 4.5.13 + 4.5.14 io.github.dan2097 jna-inchi-all - 1.1 + 1.2 org.junit.jupiter junit-jupiter-engine ${junit-version} - + org.jfree jfreechart - 1.5.3 + 1.5.4 org.jfree @@ -303,7 +308,7 @@ org.springframework.boot spring-boot-maven-plugin - 2.7.0 + ${spring-boot.version} diff --git a/bump-version.sh b/bump-version.sh index a7845057..cb9bbdb0 100755 --- a/bump-version.sh +++ b/bump-version.sh @@ -1,2 +1,3 @@ #!/bin/bash mvn -f MassBank-Project/pom.xml build-helper:parse-version versions:set -DnewVersion=$1 +mvn -f MassBank-Project/pom.xml versions:set-property -Dproperty=timestamp -DnewVersion=`date --iso-8601=seconds` diff --git a/compose/ServerInfo.properties b/compose/ServerInfo.properties new file mode 100644 index 00000000..d66e5e8a --- /dev/null +++ b/compose/ServerInfo.properties @@ -0,0 +1 @@ +server.info=Apache Tomcat diff --git a/compose/full-service.yml b/compose/full-service.yml index 2a129639..f5179cd4 100644 --- a/compose/full-service.yml +++ b/compose/full-service.yml @@ -17,6 +17,7 @@ services: - $PWD/MassBank-Project/MassBank-web/target/MassBank.war:/usr/local/tomee/webapps/MassBank.war - $PWD/conf/full-service.conf:/etc/massbank.conf - $PWD/../MassBank-data:/MassBank-data + - $PWD/compose/ServerInfo.properties:/usr/local/tomee/lib/org/apache/catalina/util/ServerInfo.properties ports: - "808${TAG}:8080" restart: always diff --git a/install.sh b/install.sh index bfdb3131..761cc2b2 100755 --- a/install.sh +++ b/install.sh @@ -26,7 +26,7 @@ case $1 in docker-compose -f compose/full-service.yml -p $TAG build docker-compose -f compose/full-service.yml -p $TAG up -d mariadb docker-compose -f compose/full-service.yml -p $TAG exec mariadb /root/waitforSQL.sh - docker-compose -f compose/full-service.yml -p $TAG run --rm maven mvn -q -Duser.home=/var/maven -f /project clean package + CURRENT_UID=$(id -u):$(id -g) docker-compose -f compose/full-service.yml -p $TAG run --rm maven mvn -q -Duser.home=/var/maven -f /project clean package docker-compose -f compose/full-service.yml -p $TAG up -d tomee docker-compose -f compose/full-service.yml -p $TAG \ run --rm dbupdate \ @@ -42,7 +42,7 @@ case $1 in ;; deploy) docker-compose -f compose/full-service.yml -p $TAG pull - docker-compose -f compose/full-service.yml -p $TAG run --rm maven mvn -q -Duser.home=/var/maven -f /project clean package + CURRENT_UID=$(id -u):$(id -g) docker-compose -f compose/full-service.yml -p $TAG run --rm maven mvn -q -Duser.home=/var/maven -f /project clean package docker-compose -f compose/full-service.yml -p $TAG rm -s tomee docker-compose -f compose/full-service.yml -p $TAG up -d tomee ;; diff --git a/modules/sql/docker-entrypoint-initdb.d/01-init-massbank.sql b/modules/sql/docker-entrypoint-initdb.d/01-init-massbank.sql index b14de124..01eb6990 100644 --- a/modules/sql/docker-entrypoint-initdb.d/01-init-massbank.sql +++ b/modules/sql/docker-entrypoint-initdb.d/01-init-massbank.sql @@ -94,6 +94,7 @@ CREATE TABLE INSTRUMENT ( CREATE TABLE RECORD ( ACCESSION VARCHAR(255) NOT NULL UNIQUE, + RECORD_TIMESTAMP TIMESTAMP, RECORD_TITLE VARCHAR(600) NOT NULL, DATE VARCHAR(600) NOT NULL, AUTHORS VARCHAR(600) NOT NULL, @@ -250,7 +251,7 @@ CREATE TABLE ANNOTATION ( ); CREATE TABLE LAST_UPDATE ( - TIME TIMESTAMP, + LAST_UPDATE TIMESTAMP, VERSION VARCHAR(100) );