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Nucleic Acids Research· 2024Q1

The PRIDE database at 20 years: 2025 update

Yasset Pérez‐Riverol, Chakradhar Bandla, Deepti J Kundu, Selvakumar Kamatchinathan et al.

Short summary

The PRIDE database, a leading MS-based proteomics data repository, has seen a 534 dataset/month submission rate increase due to infrastructure upgrades like Globus and automated validation.

AI-generated from the title and abstract; the full text is not read.

Key points

  • PRIDE Archive receives an average of 534 new datasets per month.
  • Infrastructure improvements include Globus for large data transfers and an automatic dataset validation process.
  • New developments include a PRIDE chatbot powered by Large Language Models.
  • Enhanced support for MS crosslinking datasets is now available.
  • Increased efforts focus on reusing and disseminating proteomics data into resources like UniProt.

AI-generated from the title and abstract; the full text is not read.

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.

The authors' abstract, as published at the source. Nucleic Acids Research, 2024 · DOI ↗

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