Software

Proteomics Software From PROBE

To the right 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.

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.

PeptideShaker

Interpretation of proteomics identifications from multiple search engines
SearchGUI

Graphical user interface for proteomics identification search engines
compomics-utilities

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
MassShiftFinder

Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.
MassSorter

Administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
POSTMan

POST-translational modification analysis
PklFileMerger

Conversion of single Q-TOF pkl-files into larger mergefiles before database searching