© The Author 2015. Published by Oxford University Press. 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.
Perez-Riverol, Y., Uszkoreit, J., Sanchez, A., Ternent, T., Del Toro, N., Hermjakob, H., … Wang, R. (2015). Ms-Data-Core-Api: An open-source, metadata-oriented library for computational proteomics. Bioinformatics, 31(17), 2903–2905. https://doi.org/10.1093/bioinformatics/btv250