PRIDE: The proteomics identifications database

TLDR

High‑throughput proteomics has produced vast numbers of protein identifications, yet the resulting lists are typically published as cumbersome PDF files that are difficult for computational tools to parse. The authors introduce PRIDE, a database designed to make publicly available proteomics identifications easily accessible and searchable. PRIDE provides a web‑based query interface, a user‑friendly upload portal, an API, and freely downloadable source code and data for local use.

Abstract

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.