The PRIDE database at 20 years: 2025 update

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.

Authors

Institutions

Publication Details

Journal
Nucleic Acids Research
Published
2024-11-04
DOI
https://doi.org/10.1093/nar/gkae1011
Citations
1,352
Primary Topic
Research Data Management Practices
Type
article
Field-Weighted Citation Impact
1052.62

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

The PRIDE database at 20 years: 2025 update

Shengbo Wang, Mathias Walzer, Deepti J Kundu, Chakradhar Bandla et al.
1,352 citations
Nucleic Acids Research
Research Data Management Practices
1052.62
article

The PRIDE database at 20 years: 2025 update

Shengbo Wang, Mathias Walzer, Deepti J Kundu, Chakradhar Bandla, Suresh Hewapathirana, Ananth Prakash, Juan Antonio Vizcaíno, Yasset Pérez‐Riverol, Nithu Sara John, Selvakumar Kamatchinathan, Jingwen Bai
article en
1,352 citations

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.

Nucleic Acids ResearchVol. 53(D1)
European Bioinformatics Institute (GB), Wellcome Trust (GB)
Wellcome, Wellcome Trust, UK Research and Innovation, European Commission, Fonds National de la Recherche Luxembourg, Directorate for Biological Sciences, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council
Industry, innovation and infrastructure
Openalex Percentile: Top 0%
Research Data Management Practices
1052.62
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.