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PRIDE Proteomes: a Condensed View of the Plethora of Public Proteomics Data Available in the PRIDE Repository

This paper is available in a repository.
This paper is available in a repository.

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Abstract

The PRIDE (PRoteomics IDEntifications) database [1] (http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute (EBI, Cambridge, UK) is one of the main public repositories for mass spectrometry (MS)-based proteomics data. In PRIDE, the amount of data is constantly growing at a very significant pace. Apart from the data management component, the other main challenge in proteomics resources such as PRIDE is to provide an aggregated and quality-scored version of the peptide/protein identifications found across all the submitted projects, in order to decide which information is more reliable. PRIDE Proteomes is a new resource providing a condensed, protein centric view of the MS data in PRIDE. As part of the new project a scheme for quality scoring is being developed at present. The information that is used for this aim is the experimental metadata annotation, the number of evidences and the resulting data after applying the 'PRIDE Cluster' [2] algorithm. This scoring will be then propagated to the peptide and protein level by using a set of defined rules. A beta version of PRIDE Proteomes is now available for four species (human, rat, mouse and Arabidopsis) at http://wwwdev.ebi.ac.uk/pride/proteomes.