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The PRIDE database at 20 years: 2025 update.

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The PRoteomics IDEntifications (PRIDE) database enhances proteomics data sharing with improved infrastructure and novel tools like a chatbot. It now supports over 534 datasets monthly, boosting data accessibility and reuse.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Data Science

Background:

  • The PRoteomics IDEntifications (PRIDE) database is a leading repository for mass spectrometry (MS)-based proteomics data.
  • It is a key member of the ProteomeXchange consortium, facilitating data standardization and sharing.
  • Continuous development is essential to manage the growing volume of proteomics data.

Purpose of the Study:

  • To summarize recent developments and improvements in the PRIDE database and its associated tools over the past three years.
  • To highlight advancements in infrastructure, data submission pipelines, and novel features.
  • To showcase efforts in data reuse and dissemination to other valuable biological resources.

Main Methods:

  • Infrastructure enhancements including Globus for large file transfers and automated validation processes.
  • Development of a new data resubmission pipeline.
  • Integration of open-source Large Language Models for a PRIDE chatbot and improved support for MS crosslinking data.

Main Results:

  • PRIDE Archive receives an average of 534 new datasets per month, indicating increased data submission.
  • Significant improvements in data submission, validation, and transfer efficiency.
  • Introduction of a chatbot and enhanced support for specialized datasets like crosslinking experiments.

Conclusions:

  • PRIDE has successfully scaled its infrastructure and introduced innovative tools to manage and support the growing volume of proteomics data.
  • These advancements facilitate easier data submission, validation, and accessibility.
  • Enhanced data reuse and dissemination into resources like UniProt and Ensembl maximize the value of submitted proteomics data.