@article{Perez-Riverol2015, 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.}, author = {Perez-Riverol, Yasset and Uszkoreit, Julian and Sanchez, Aniel and Ternent, Tobias and del Toro, Noemi and VizcaĆ­no, Juan Antonio and Wang, Rui and Hermjakob, Henning}, doi = {10.1093/bioinformatics/btv250}, journal = {Bioinformatics}, month = {apr}, pages = {2903-2905}, title = {ms-data-core-api: An open-source, metadata-oriented library for computational proteomics.}, url = {https://academic.oup.com/bioinformatics/article-pdf/31/17/2903/17085007/btv250.pdf}, volume = {31}, year = {2015} }