The PRIDE database at 20 years: 2025 update

Yasset Pérez‐Riverol(European Bioinformatics Institute), Chakradhar Bandla(European Bioinformatics Institute), Deepti J Kundu(European Bioinformatics Institute), Selvakumar Kamatchinathan(European Bioinformatics Institute), Jingwen Bai(European Bioinformatics Institute), Suresh Hewapathirana(European Bioinformatics Institute), Nithu Sara John(European Bioinformatics Institute), Ananth Prakash(European Bioinformatics Institute), Mathias Walzer(European Bioinformatics Institute), Shengbo Wang(European Bioinformatics Institute), Juan Antonio Vizcaíno(European Bioinformatics Institute)
Nucleic Acids Research
November 4, 2024
10.1093/nar/gkae1011
Cited by 1,562Open Access
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Abstract

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's leading mass spectrometry (MS)-based proteomics data repository and one of the founding members of the ProteomeXchange consortium. This manuscript summarizes the developments in PRIDE resources and related tools for the last three years. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 534 datasets per month. This has been possible thanks to continuous improvements in infrastructure such as a new file transfer protocol for very large datasets (Globus), a new data resubmission pipeline and an automatic dataset validation process. Additionally, we will highlight novel activities such as the availability of the PRIDE chatbot (based on the use of open-source Large Language Models), and our work to improve support for MS crosslinking datasets. Furthermore, we will describe how we have increased our efforts to reuse, reanalyze and disseminate high-quality proteomics data into added-value resources such as UniProt, Ensembl and Expression Atlas.

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