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ProteoSuite specifications


Unique identifier OMICS_24188
Name ProteoSuite
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Apache License version 2.0
Computer skills Medium
Version 0.3.6
Stability Alpha
Maintained Yes




No version available



  • person_outline Andrew Jones
  • person_outline Faviel Gonzalez-Galarza

Additional information

Publication for ProteoSuite

ProteoSuite citations


The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

PMCID: 4973685
PMID: 26037908
DOI: 10.1002/pmic.201400535

[…] e graphical user interface (GUI) embedded in the mzqViewer – enabling end users to run single routines independently. We will later be releasing a full software package for proteomics analysis called ProteoSuite (, which will include the mzqLibrary, mzqViewer and quantitation by label‐free or tag‐based (iTRAQ/TMT) approaches. […]


Universal database search tool for proteomics

Nat Commun
PMCID: 5036525
PMID: 25358478
DOI: 10.1038/ncomms6277

[…] ell before this paper was prepared for a journal submission, MS-GF+ has already been integrated into the following pipelines and statistical modeling tools: Trans-Proteomics Pipeline [], Galaxy-P [], ProteoSuite [], IDPicker [], SearchGUI [], Scaffold [], ProteoSAFe, Skyline [], and Percolator [, ]. Peptide identification tools that combine the results of multiple database search tools such as MSb […]


Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

Biochim Biophys Acta
PMCID: 3898926
PMID: 23467006
DOI: 10.1016/j.bbapap.2013.02.032

[…] ein lists, sort them according to different Mascot parameters (such as the score and the rank order of the identified peptides), and to validate the results.X-Tracker ( and ProteoSuite ( are Java frameworks for the analysis of quantitative proteomics data. X-Tracker is able to support quantitation data coming from many different approaches, b […]


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ProteoSuite institution(s)
Institute of Integrative Biology, University of Liverpool, Liverpool, UK; Faculty of Life Sciences, University of Manchester, Manchester, UK; Bioinformatics Group, Cranfield Health, Cranfield University, Cranfield, UK; EMBL-The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
ProteoSuite funding source(s)
Supported by the British Biotechnology and Biological Sciences Research Council (grants BB/I00095X/1, BB/I000909/1, BB/I000631/1, and BB/I001131/).

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