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compomics-utilities: an open-source Java library for computational proteomics

Harald Barsnes12, Marc Vaudel3, Niklaas Colaert45, Kenny Helsens45, Albert Sickmann3, Frode S Berven1 and Lennart Martens45*

Author Affiliations

1 Proteomics Unit, Department of Biomedicine, University of Bergen, Norway

2 Computational Biology Unit, UniComputing, Bergen, Norway

3 Leibniz - Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany

4 Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium

5 Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium

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BMC Bioinformatics 2011, 12:70  doi:10.1186/1471-2105-12-70

Published: 8 March 2011



The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool.


In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development.


As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.