This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.
The remaining content of this README file remained unmodified.
MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rules
The program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0. Please contact Hiroshi Tsugawa ([email protected]) for feedback, bug reports, and questions or create an issue on this GitHub repository.
Lead developer: Hiroshi Tsugawa (RIKEN) Current main developers: Hiroshi Tsugawa (RIKEN), Ipputa Tada (SOKENDAI), and Yuki Matsuzawa (RIKEN) Past developers: Diego Pedrosa (UC Davis)
- .net framework 4.8
- nuget.exe (https://www.nuget.org/downloads)
Clone the github directory
git clone https://github.com/RECETOX/recetox-msfinder.git
From the project root run
nuget.exe restore
dotnet build .\MsfinderConsoleApp\
Required args:
| Args | Description |
|---|---|
| -i | input folder/file to be processed |
| -m | method file holding processing properties |
| -o | output folder to save results |
example:
MsfinderConsoleApp.exe annotate -i <input folder> -m <method file> -o <output file>
MsfinderConsoleApp.exe annotate -i test.msp -m MSFINDER.INI -o out.msp
The LBM (*.LBM2) file contains the in silico MS/MS spectra of lipids. There are currently three files named with 'FiehnO (Oliver Fiehn laboratory)', 'AritaM (Makoto Arita laboratory)', and 'SaitoK (Kazuki Saito laboratory)'. These files contain the same MS/MS spectra information but have different predicted retention times which were optimized for the indivisual method. One of the '.LBM' files which contains lipid's in silico MS/MS should be also in the same folder as 'MSDIAL.exe' for Lipidomics project.
MRMPROBS software suite is sutable for targeted metabolomics and lipidomics, and it also supports MRM/SRM data. http://prime.psc.riken.jp/compms/mrmprobs/main.html
This is the source code for msdial version 4.18 and msfinder version 3.32. The source code is licensed under GNU LESSER GENERAL PUBLIC LICENSE (LGPL) version 3. See LGPL.txt for full text of the license. This software uses third-party software. A full list of third-party software licenses in MsdialWorkbench is in the file THIRD-PARTY-LICENSE-README.txt.