The PRIDE database and related tools and resources in 2019: improving support for quantification data

Yasset Pérez‐Riverol(European Bioinformatics Institute), Attila Csordás(European Bioinformatics Institute), Jingwen Bai(European Bioinformatics Institute), Manuel Bernal Llinares(European Bioinformatics Institute), Suresh Hewapathirana(European Bioinformatics Institute), Deepti J Kundu(European Bioinformatics Institute), Avinash Inuganti(European Bioinformatics Institute), Johannes Griss(European Bioinformatics Institute), Gerhard Mayer(Ruhr University Bochum), Martin Eisenacher(Ruhr University Bochum), Enrique Pérez(European Bioinformatics Institute), Julian Uszkoreit(Ruhr University Bochum), Julianus Pfeuffer(University of Tübingen), Timo Sachsenberg(University of Tübingen), Şule Yılmaz(Max Planck Institute of Biochemistry), Shivani Tiwary(Max Planck Institute of Biochemistry), Jürgen Cox(Max Planck Institute of Biochemistry), Enrique Audain(University Hospital Schleswig-Holstein), Mathias Walzer(European Bioinformatics Institute), Andrew F. Jarnuczak(European Bioinformatics Institute), Tobias Ternent(European Bioinformatics Institute), Alvis Brāzma(European Bioinformatics Institute), Juan Antonio Vizcaíno(European Bioinformatics Institute)
Nucleic Acids Research
October 22, 2018
10.1093/nar/gky1106
Cited by 7,384Open Access
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Abstract

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.

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