-
Notifications
You must be signed in to change notification settings - Fork 5
/
Copy pathindex.html
109 lines (89 loc) · 5.63 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
---
layout: main
title: home
nav:
home: active
container: none
---
<div id='home-header'>
</div>
<div class="container">
<div class="row">
<div class="col-sm-6 col-md-3">
<h2>MetFrag Web</h2>
<p><a class="btn btn-primary" href="/MetFrag/projects/metfragweb" role="button">Learn more</a></p>
<p>Use <a href="https://msbi.ipb-halle.de/MetFrag/">MetFrag</a> directly from your browser for a visual,
interactive experience. Great for beginners or exploring your data</p>
</div>
<div class="col-sm-6 col-md-3">
<h2>MetFrag CL</h2>
<p><a class="btn btn-primary" href="/MetFrag/projects/metfragcl" role="button">Learn more</a></p>
<p>Use the <a href="/MetFrag/projects/metfragcl">MetFrag command line tool</a> for batch processing and
additional features. See detailed documentation for settings</p>
</div>
<div class="col-sm-6 col-md-3">
<h2>MetFrag in R</h2>
<p><a class="btn btn-primary" href="/MetFrag/projects/metfragr" role="button">Learn more</a></p>
<p>Users familiar with R can download the <a href="https://github.com/ipb-halle/MetFragR">MetFragR</a>
R-package, or use MetFrag built into the <a href="https://rickhelmus.github.io/patRoon/">patRoon</a> workflow</p>
</div>
<div class="col-sm-6 col-md-3">
<h2>Converter</h2>
<p><a class="btn btn-primary" href="/MetFrag/projects/converter" role="button">Learn more</a></p>
<p>Tools to convert between MetFrag-related file formats, including MassBank to MetFrag and SDF to XLS</p>
</div>
</div>
<h3>Overview</h3>
<p>MetFrag is a freely available software to annotate metabolites and other small molecules using
fragmentation information from tandem mass spectra, which is a first and critical step towards
identification of a molecule's structure. Candidate molecules can be retrieved from
different databases using mass or molecular formula and are then fragmented in silico
and matched against the fragments. The resulting score calculated using the fragment peak matches
can be used to rank the various candidate molecules. Additional scoring terms, including an
experimental mass spectral library match, or database-specific scoring terms such as
patent and literature values can be defined in the settings. </p>
<h3>Availability</h3>
<p>MetFrag can be easily used via the <a href="https://msbi.ipb-halle.de/MetFrag/">web interface</a>
as documented <a href="/MetFrag/projects/metfragweb">here</a>.
The MetFrag Command Line version (latest release
<a href="https://github.com/ipb-halle/MetFragRelaunched/releases/latest">here</a>;
documented <a href="/MetFrag/projects/metfragcl">here</a>)
is available for high-throughput data processing options.
For R users, options include the <a href="/MetFrag/projects/metfragr">MetFragR R-package</a>
and the integrated non-target screening workflow <a href="https://rickhelmus.github.io/patRoon/">patRoon</a>.</p>
<h3>Citing MetFrag</h3>
<p>Please cite this article when using MetFrag: </p>
<p>C Ruttkies, EL Schymanski, S Wolf, J Hollender, S Neumann (2016)
<a href="https://doi.org/10.1186/s13321-016-0115-9">MetFrag relaunched: incorporating strategies beyond in silico fragmentation</a>
Journal of Cheminformatics 8:3. DOI: <a href="https://doi.org/10.1186/s13321-016-0115-9">10.1186/s13321-016-0115-9</a>
</p>
<h3>Other MetFrag Publications</h3>
<p><b>Exposomics - MetFrag Meets PubChemLite: </b>
EL Schymanski, T Kondic, S Neumann, PA Thiessen, J Zhang, EE Bolton (2021)
<a href="https://doi.org/10.1186/s13321-021-00489-0">Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag</a>
Journal of Cheminformatics 13:19. DOI: <a href="https://doi.org/10.1186/s13321-021-00489-0">10.1186/s13321-021-00489-0</a>
</p>
<p><b>MetFrag with Statistical Fragment Learning:</b>
C Ruttkies, S Neumann, S Posch (2019)
<a href="https://doi.org/10.1186/s12859-019-2954-7">Improving MetFrag with statistical learning of fragment annotations</a>:
BMC Bioinformatics 20: 376. DOI: <a href="https://doi.org/10.1186/s12859-019-2954-7">10.1186/s12859-019-2954-7</a> </p>
<p><b>MetFrag and HD Exchange:</b>
C Ruttkies, EL Schymanski, N Strehmel, J Hollender, S Neumann, AJ Williams, M Krauss (2019)
<a href="https://doi.org/10.1007/s00216-019-01885-0">Supporting non-target identification by adding hydrogen deuterium exchange MS/MS capabilities to MetFrag</a>:
Analytical and Bioanalytical Chemistry 411(19), 4683–4700.
DOI: <a href="https://doi.org/10.1007/s00216-019-01885-0">10.1007/s00216-019-01885-0</a> </p>
<p><b>MetFrag Relaunched (2016): </b>
C Ruttkies, EL Schymanski, S Wolf, J Hollender, S Neumann (2016)
<a href="https://doi.org/10.1186/s13321-016-0115-9">MetFrag relaunched: incorporating strategies beyond in silico fragmentation</a>
Journal of Cheminformatics 8:3. DOI: <a href="https://doi.org/10.1186/s13321-016-0115-9">10.1186/s13321-016-0115-9</a>
</p>
<p><b>Original MetFrag Version (2010):</b>
S Wolf, S Schmidt, M Müller-Hannemann, S Neumann (2010)
<a href="https://doi.org/10.1186/1471-2105-11-148">In silico fragmentation for computer assisted identification of metabolite mass spectra</a>:
BMC Bioinformatics 11:148. DOI: <a href="https://doi.org/10.1186/1471-2105-11-148">10.1186/1471-2105-11-148</a>.
Here are the papers that have cited MetFrag (version 2010) so far in
<a href="http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=20307295">PubMed</a>
and <a href="http://scholar.google.com/scholar?oi=bibs&hl=en&cites=10278388642349466161&as_sdt=5">Google Scholar</a>. </p>
<h3>License</h3>
<p>MetFrag is published under a <a href="http://www.gnu.org/licenses/lgpl.html">GNU Lesser General Public License</a> version 2.1 or later.</p>
</div>