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

Yasset Perez‐Riverol ,Julian Uszkoreit,Avinash Inuganti,Tobias Ternent,Mathias Walzer,Suresh Hewapathirana,Gerhard Mayer,Manuel Bernal-Llinares,Enrique Audain,Timo Sachsenberg,Martin Eisenacher,Şule Yılmaz,Enrique Pérez,Johannes Griss,Julianus Pfeuffer,Shivani Tiwary,Juan Antonio Vizcaíno,Andrew F Jarnuczak ,Attila Csordás ,Juergen Cox ,Alvis Brāzma ,Deepti Jaiswal Kundu ,Jinwen Bai

doi:10.1093/nar/gky1106

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.

Highlights

High-throughput mass spectrometry (MS)-based proteomics approaches have matured significantly in recent years, becoming an increasingly used tool in biological research, sometimes together with other ‘omics’ approaches such as genomics and transcriptomics
We summarize the developments in PRoteomics IDEntifications (PRIDE) resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016
The PRoteomics IDEntifications (PRIDE) database was set up in 2004 at the European Bioinformatics Institute (EMBL-EBI, Hinxton, Cambridge, UK) to enable public data deposition of MS proteomics data, providing access to the experimental data described in scientific publications [1]

Summary

Introduction

High-throughput mass spectrometry (MS)-based proteomics approaches have matured significantly in recent years, becoming an increasingly used tool in biological research, sometimes together with other ‘omics’ approaches such as genomics and transcriptomics. To what happened in those fields, in the last 15 years several public proteomics repositories and bioinformatics resources have been developed to support proteomics researchers. The PRoteomics IDEntifications (PRIDE) database (https: //www.ebi.ac.uk/pride/) was set up in 2004 at the European Bioinformatics Institute (EMBL-EBI, Hinxton, Cambridge, UK) to enable public data deposition of MS proteomics data, providing access to the experimental data described in scientific publications [1]. PRIDE (more concretely its archival component, PRIDE Archive) has evolved in parallel with the field becoming the largest proteomics data repository worldwide [2].

Objectives

Conclusion