title: ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
abstract: 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.
  
  
  METHODS
  The software is freely available at https://github.com/PRIDE-Utilities/ms-data-core-api.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online
  
  
  BACKGROUND
  juan@ebi.ac.uk.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Yasset
authors.initials: Y
authors.lastname: Perez-Riverol
authors.affiliation: Ruhr-Universität Bochum, Medizinisches Proteom-Zenter, Medical Bioinformatics, ZKF, E.142, Universitätsstr. 150, D-44801 Bochum, Germany and.
authors.forename: Julian
authors.initials: J
authors.lastname: Uszkoreit
authors.affiliation: Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba.
authors.forename: Aniel
authors.initials: A
authors.lastname: Sanchez
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Tobias
authors.initials: T
authors.lastname: Ternent
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Noemi
authors.initials: N
authors.lastname: Del Toro
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D010446:Peptide Fragments / Q000032:analysis; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D057188:Workflow
chemical_list: D010446:Peptide Fragments; D011506:Proteins