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. 2005 Aug;5(13):3537-45.
doi: 10.1002/pmic.200401303.

PRIDE: the proteomics identifications database

Lennart Martens  1 , Henning Hermjakob, Philip Jones, Marcin Adamski, Chris Taylor, David States, Kris Gevaert, Joël Vandekerckhove, Rolf Apweiler
Affiliations

PRIDE: the proteomics identifications database

Lennart Martens et al. Proteomics. 2005 Aug.

Erratum in

  • Proteomics. 2005 Oct;5(15):4046

Abstract

The advent of high-throughput proteomics has enabled the identification of ever increasing numbers of proteins. Correspondingly, the number of publications centered on these protein identifications has increased dramatically. With the first results of the HUPO Plasma Proteome Project being analyzed and many other large-scale proteomics projects about to disseminate their data, this trend is not likely to flatten out any time soon. However, the publication mechanism of these identified proteins has lagged behind in technical terms. Often very long lists of identifications are either published directly with the article, resulting in both a voluminous and rather tedious read, or are included on the publisher's website as supplementary information. In either case, these lists are typically only provided as portable document format documents with a custom-made layout, making it practically impossible for computer programs to interpret them, let alone efficiently query them. Here we propose the proteomics identifications (PRIDE) database (http://www.ebi.ac.uk/pride) as a means to finally turn publicly available data into publicly accessible data. PRIDE offers a web-based query interface, a user-friendly data upload facility, and a documented application programming interface for direct computational access. The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation.

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