title: 2016 update of the PRIDE database and its related tools.
abstract: The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development 'PRIDE Cluster' and 'PRIDE Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK juan@ebi.ac.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: Attila
authors.initials: A
authors.lastname: Csordas
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: José A
authors.initials: JA
authors.lastname: Dianes
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria.
authors.forename: Johannes
authors.initials: J
authors.lastname: Griss
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Ilias
authors.initials: I
authors.lastname: Lavidas
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Mayer
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: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
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 Department of Computer Science and Technology, Hubei University of Education, Wuhan, China.
authors.forename: Qing-Wei
authors.initials: QW
authors.lastname: Xu
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
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK National Center for Protein Sciences, Beijing, China.
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
mesh_terms: D030562:Databases, Protein; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics; D012984:Software; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D011506:Proteins