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