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Oxford University Press (OUP), Bioinformatics, 17(31), p. 2903-2905

DOI: 10.1093/bioinformatics/btv250

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ms-data-core-api: An open-source, metadata-oriented library for computational proteomics.

Journal article published in 2015 by Yasset Perez-Riverol, Julian Uszkoreit, Aniel Sanchez, Tobias Ternent, Noemi del Toro, Juan Antonio Vizcaíno, Henning Hermjakob ORCID, Rui Wang
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Summary: The ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines. The Application Programming Interface, written in Java, enables rapid tool creation by providing a robust, pluggable programming interface and common data model. The data model is based on controlled vocabularies/ontologies and captures the whole range of data types included in common proteomics experimental workflows, going from spectra to peptide/protein identifications to quantitative results. The library contains readers for three of the most used Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab. In addition to mzML, it also supports other common mass spectra data formats: dta, ms2, mgf, pkl, apl (text-based), mzXML and mzData (XML-based). Also, it can be used to read PRIDE XML, the original format used by the PRIDE database, one of the world-leading proteomics resources. Finally, we present a set of algorithms and tools whose implementation illustrates the simplicity of developing applications using the library.