The PRIDE database at 20 years: 2025 update

2024/11/04 by Yasset Pérez‐Riverol, Chakradhar Bandla, Deepti J Kundu +8 · 81 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · Decision Sciences · #Genetics, Bioinformatics, and Biomedical Research #Research Data Management Practices #Scientific Computing and Data Management

paper · pdf · doi:10.1093/nar/gkae1011

openalex publication_date 2024/11/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

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.

Citations

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• The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
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