Software
Proteomics Software From PROBE
Below is a list of software where current or previous members of the PROBE team has contributed in the development.
All the proteomics software presented here may be downloaded and used free of charge. But please include a reference to the manuscript describing the software and/or a link to the software when using it as part of a publication.
In depth tutorials on Bioinformatics for Proteomics using some of the tools below can be found here: http://compomics.com/bioinformatics-for-proteomics.
For questions, please contact the authors of the tools (see the tool's Google Code page for details).
For questions regarding POSTMan and PklFileMerger, please send an email to Magnus Arntzen.
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PeptideShaker
Interpretation of proteomics identifications from multiple search engines
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SearchGUI
Graphical user interface for proteomics identification search engines
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compomics-utilities
Java library encompassing shared code of various mass spectrometry research projects
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Fragmentation Analyzer
Standalone Java tool for analyzing MS/MS fragmentation data
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PRIDE Converter
Data conversion tool for creating PRIDE XML
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OLS Dialog
Java front end to the Ontology Lookup Service
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OMSSA Parser
Java based parser for OMSSA omx files
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XTandem Parser
Java based parser for X!Tandem output xml files
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MassShiftFinder
Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.
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MassSorter
Administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
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POSTManSmall images:
POST-translational modification analysis
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PklFileMergerSmall images:
Conversion of single Q-TOF pkl-files into larger mergefiles before database searching
