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Related Experiment Videos

PRIDE: new developments and new datasets.

Philip Jones1, Richard G Côté, Sang Yun Cho

  • 1EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. pjones@ebi.ac.uk

Nucleic Acids Research
|November 24, 2007
PubMed
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The PRIDE database has significantly expanded its protein and peptide identification data and improved user tools. New features facilitate data submission and querying, enhancing proteomic research accessibility.

Area of Science:

  • Proteomics
  • Bioinformatics
  • Mass Spectrometry Data Management

Background:

  • The PRIDE database, a public repository for protein and peptide identifications, has seen substantial growth since its 2006 description.
  • Significant datasets from the HUPO Brain and Liver Proteome Projects have been incorporated.
  • Previous versions required improvements in data submission and querying capabilities.

Purpose of the Study:

  • To detail the advancements in the PRIDE database, focusing on data expansion and enhanced usability.
  • To introduce new tools and interfaces for improved data submission and complex querying.
  • To report on collaborations extending PRIDE's functionality, such as incorporating iTRAQ quantitative data.

Main Methods:

  • Expansion of the PRIDE relational database with new proteomic datasets.

Related Experiment Videos

  • Development of a Microsoft Excel workbook for streamlined data collation and PRIDE XML generation.
  • Integration of a BioMart interface to enable complex data querying.
  • Implementation of methods to encode iTRAQ quantitative data within PRIDE XML.

    • Main Results:

    • The volume of public data in PRIDE has increased by over tenfold.
    • New user interface features simplify data submission.
    • Enhanced querying mechanisms, including BioMart, improve data accessibility.
    • Successful encoding of iTRAQ quantitative data into PRIDE XML format.

    Conclusions:

    • PRIDE has evolved into a more comprehensive and user-friendly resource for proteomic data.
    • The implemented tools and interfaces facilitate broader participation and deeper data analysis in proteomics.
    • Continued development and collaboration enhance PRIDE's utility for the scientific community.