compomics-utilities publication:

What is compomics-utilities?

The Computational Omics and Systems Biology Group develops various bioinformatics tools for analyzing omics data.

compomics-utilities is a library containing code shared by many of our research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. We believe that this library can be of use to other research groups doing computational proteomics, and have therefore made it available as open source.

Go to top of page

Projects using compomics-utilities

Project Description Publication
PeptideShaker interpretation of proteomics identification results Vaudel et al: Nature Biotechnol. 2015 Jan;33(1):22–24.
MetaProteomeAnalyzer analyzing meta-proteomics data Muth et al: J Proteome Res. 2015 (in press).
DeNovoGUI de novo sequencing of tandem mass spectra Muth at al: J Proteome Res. 2014 Feb 7;13(2):1143-6.
pride-asap uniform annotation of identified spectra stored in PRIDE Hulstaert et al: J Proteomics. 2013 Apr 17
ProteoCloud proteomics cloud computing pipeline Muth et al: J Proteomics. 2013 Aug 2;88:104-8
thermo-msf-parser parser and viewer for thermo msf files Colaert et al: J Proteome Res. 2011;10(8):3840-3
SearchGUI graphical user interface for proteomics identification search engines Barsnes et al: J Proteome Res. 2018 (in press) Vaudel et al: Proteomics 2011;11(5):996-9
XTandem Parser java parser for X!Tandem output xml files Muth et al: Proteomics 2010;10(7):1522-4
jmzML java implementation of the PSI-MS mzML specification Côté et al: Proteomics 2010;10(7):1332-5
Fragmentation Analyzer analyzing MS/MS fragmentation data Barsnes et al: Proteomics 2010;10(5):1087-90
ms_lims mass spectrometry based proteomics information management system Helsens et al: Proteomics 2010;10(6):1261-4
Rover visualize and validate quantitative proteomics data Colaert et al: Proteomics 2010;10(6):1226-9
IceLogo next-generation visualization of protein consensus sequences Colaert et al: Nature Methods 2009;6(11):786-7
OMSSA Parser java parser for OMSSA omx files Barsnes et al: Proteomics 2009;9(14):3772-4
Peptizer automating manual validation of MS/MS search results Helsens et al: MCP 2008;7(12):2363-72
MascotDatfile java API for MS/MS search results by Mascot Helsens et al: Proteomics 2007;7(3):364-6
DBToolkit manipulating fasta sequence databases Martens et al: Bioinformatics 2005;21(17):3584-5
MetaNovo a probabilistic approach to peptide and polymorphism discovery in complex mass spectrometry datasets Potgieter et al: BioRxiv 2019;605550

Go to top of page

Using compomics-utilities

For example code and demos showing how the compomics-utilities library can be used in your project see Examples. Also check the JavaDoc.

Go to top of page


We strongly recommend Maven when using compomics-utilities, as this makes sure that one gets all the dependencies right. See Maven Dependency below.

All compomics-utilities builds are available here.

See also the JavaDoc.

If you for some reason cannot use Maven and need a complete build of compomics-utilities, please let us know and we will send you the latest build as a zip file.

Go to top of page

Maven Dependency

compomics-utilities is available for use in Maven projects:


    <!-- Compomics Genesis Maven 2 repository -->
        <name>Genesis maven2 repository</name>

    <!-- old EBI repository -->
        <name>The EBI internal repository</name>

    <!-- EBI repository -->
        <name>EBI Nexus Repository</name>

Update the version number to latest released version, see the Maven repository.

Go to top of page


(Click on figure to see the full size version)


Go to top of page