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

TLDR

PRIDE, the world’s largest mass‑spectrometry proteomics data repository and a founding member of ProteomeXchange, has become the standard for public data sharing and reuse in the field over the past three years. This manuscript reviews the advances in PRIDE resources and related tools since the 2016 Nucleic Acids Research update. We describe PRIDE Archive’s new scalable, fault‑tolerant architecture, including a modern storage backend, API, and web interface, and highlight enhanced support for quantitative proteomics via the mzTab format. Current statistics show growing data volumes and download rates, with PRIDE data increasingly integrated into resources such as Ensembl, UniProt, and Expression Atlas.

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.