The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.

Related collections

Author and article information

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (iso-abbrev): Nucleic Acids Res

Journal ID (publisher-id): nar

Journal ID (hwp): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date (Print): January 2013

Publication date (Electronic): 29 November 2012

Publication date PMC-release: 29 November 2012

Volume: 41

Issue: Database issue , Database issue

Pages: D1063-D1069

Affiliations

¹EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, ²Department of Proteomics, Center for Genetic Engineering and Biotechnology, Havana, Cuba and ³CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria

Author notes

*To whom correspondence should be addressed. Tel: +44 1223 492686; Fax: +44 1223 494468; Email: pst@ 123456ebi.ac.uk

Article

Publisher ID: gks1262

DOI: 10.1093/nar/gks1262

PMC ID: 3531176

PubMed ID: 23203882

SO-VID: e0d588ac-27f2-4e60-9269-06859618520f

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.

History

Date received : 21 September 2012

Date revision received : 30 October 2012

Date accepted : 5 November 2012

Page count

Pages: 7

Comments

Comment on this article

scite_

Cited by 723

See all cited by