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.
Interpretation of proteomics identifications from multiple search engines
Graphical user interface for proteomics identification search engines
Java library encompassing shared code of various mass spectrometry research projects
Standalone Java tool for analyzing MS/MS fragmentation data
Data conversion tool for creating PRIDE XML
Java front end to the Ontology Lookup Service
Java based parser for OMSSA omx files
Java based parser for X!Tandem output xml files
Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.
Administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
POST-translational modification analysis
Conversion of single Q-TOF pkl-files into larger mergefiles before database searching