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

Fragmentation Analyzer

Standalone Java tool for analyzing MS/MS fragmentation data

PRIDE Converter

Data conversion tool for creating PRIDE XML

OLS Dialog

Java front end to the Ontology Lookup Service

OMSSA Parser

Java based parser for OMSSA omx files

XTandem Parser

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