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The PRoteomics IDEntifications (PRIDE) database now supports increased proteomics data volumes and types. Enhanced architecture and tools facilitate data sharing and reuse within the ProteomeXchange (PX) consortium.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Proteomics

Background:

  • The PRoteomics IDEntifications (PRIDE) database is a major repository for mass spectrometry-based proteomics data.
  • Public data sharing via PRIDE, a member of the ProteomeXchange (PX) consortium, has become standard practice.
  • Data re-use in proteomics research has significantly increased.

Purpose of the Study:

  • To summarize recent developments in PRIDE resources and tools since 2016.
  • To detail architectural enhancements in PRIDE Archive for scalability and broader data type support.
  • To highlight improvements in handling quantitative proteomics data and data dissemination.

Main Methods:

  • Description of the new architecture for PRIDE Archive, including storage backend and APIs.
  • Implementation of an improved data submission framework.
  • Enhanced support for quantitative proteomics data using the mzTab format.

Main Results:

  • PRIDE Archive has undergone significant architectural development to accommodate growing data volumes and types.
  • New scalable storage, APIs, and web interfaces have been implemented.
  • Improved support for quantitative proteomics data and dissemination to external resources like UniProt.

Conclusions:

  • PRIDE Archive has been successfully upgraded to handle increased data submission and diverse data types.
  • Enhanced infrastructure and features facilitate wider adoption and re-use of proteomics data.
  • PRIDE continues to be a vital resource for the global proteomics community and related bioinformatics resources.