Using the Proteomics Identifications Database (PRIDE)

Lennart Martens1, Phil Jones1, Richard Côté1

1 EMBL‐EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.8
DOI:  10.1002/0471250953.bi1308s21
Online Posting Date:  March, 2008
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Abstract

The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer‐reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE. Curr. Protoc. Bioinform. 21:13.8.1‐13.8.19. © 2008 by John Wiley & Sons, Inc.

Keywords: PRIDE; proteomics; identifications; database; repository; standards

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Data Retrieval Using the PRIDE Web Interface
  • Basic Protocol 2: Data Retrieval Using the PRIDE BioMart
  • Basic Protocol 3: Data Submission to PRIDE
  • Support Protocol 1: Preparing a PRIDE Submission Using the Proteome Harvest Excel Workbook
  • Support Protocol 2: Preparing a PRIDE Submission Using the PRIDE API
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
   Côté, R.G., Jones, P., Apweiler, R., and Hermjakob, H. 2006. The Ontology Lookup Service, a lightweight cross‐platform tool for controlled vocabulary queries. BMC Bioinformatics 7: 97.
   Jones, P., Côté, R.G., Martens, L., Quinn, A.F., Taylor, C.F., Derache, W., Hermjakob, H., and Apweiler, R. 2006. PRIDE: A public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34: D659‐D663.
   Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., and Apweiler, R. 2005. PRIDE: The proteomics identifications database. Proteomics 5: 3537‐3545.
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