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

TLDR

The PRIDE database at the European Bioinformatics Institute is a leading repository for mass‑spectrometry–based proteomics data. This review summarizes recent developments in the PRIDE database and its associated tools. The authors present updated statistics on data content by organism, peptide and protein identifications, and post‑translational modifications, describe the new PRIDE Converter 2 and PRIDE Inspector tools, and detail PRIDE’s integration with other resources through the ProteomeXchange consortium. They highlight ongoing quality‑control initiatives and outline future plans for the database and its tools.

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.