Unit

UNIT 25.4 PRIDE: Data Submission and Analysis

  1. Juan Antonio Vizcaíno,
  2. Florian Reisinger,
  3. Richard Côté,
  4. Lennart Martens

Published Online: 1 APR 2010

DOI: 10.1002/0471140864.ps2504s60

Lab Protocol Title

Current Protocols in Protein Science

Current Protocols in Protein Science

Additional Information

How to Cite

Vizcaíno, J. A., Reisinger, F., Côté, R. and Martens, L. 2010. PRIDE: Data Submission and Analysis. Current Protocols in Protein Science. 60:25.4:25.4.1–25.4.11.

Author Information

  1. European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom

Publication History

  1. Published Online: 1 APR 2010
  2. Published Print: APR 2010
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Abstract

The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories designed to store, disseminate, and analyze mass spectrometry–based proteomics datasets. In this unit, an overview of the PRIDE system is given, including its key satellite tools: the Ontology Lookup Service (OLS), the Protein Identifier Cross-Referencing Service (PICR), and Database on Demand (DoD). Also described in detail are procedures for submitting data to PRIDE, and accessing data stored in PRIDE using the BioMart interface. Finally, to demonstrate the potential of PRIDE as a source for data mining, an example protocol is provided to showcase the powerful cross-domain query capabilities available through a combination of BioMarts. Curr. Protoc. Protein Sci. 60:25.4.1-25.4.11. © 2010 by John Wiley & Sons, Inc.

Keywords:

  • PRIDE;
  • proteomics;
  • ontologies;
  • data mining;
  • BioMart
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