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. 2011 Mar 8:12:70.
doi: 10.1186/1471-2105-12-70.

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

Harald Barsnes  1 , Marc Vaudel, Niklaas Colaert, Kenny Helsens, Albert Sickmann, Frode S Berven, Lennart Martens
Affiliations

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

Harald Barsnes et al. BMC Bioinformatics. .

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

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Figures

Figure 1
Figure 1
Spectrum visualization in compomics-utilities. The display supports both peak picking and zooming. If the peaks are annotated, the annotation can be switched on or off by the user. If more than one spectrum is shown on screen, the axes can be linked to support transitive zooming and rescaling. Finally, the spectra can be exported as images in common file formats.
Figure 2
Figure 2
Using compomics-utilities simplifies proteomics pipelines. A standard pipeline (A) has to interact with multiple search engine output file formats and data structures before all data can be analyzed. With the use of compomics-utilities (B) the data from any of the specified input formats can all be loaded transparently and are ready for processing immediately.
See this image and copyright information in PMC

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