PRIDE: Data Submission and Analysis

Juan Antonio Vizcaíno1, Florian Reisinger1, Richard Côté1, Lennart Martens1

1 European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL‐EBI), Hinxton, Cambridge, United Kingdom
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 25.4
DOI:  10.1002/0471140864.ps2504s60
Online Posting Date:  April, 2010
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

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

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Pride and Satellite Tools: OLS, PICR, and DoD
  • Data Submission to Pride
  • The Pride BioMart Interface
  • Conclusions
  • Basic Protocol 1: Cross‐Resource Data Retrieval Between Pride and Ensembl Using the Biomart Interface
  • Literature Cited
  • Figures
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Barsnes, H., Vizcaíno, J.A., Eidhammer, I., and Martens, L. 2009. PRIDE Converter: Making proteomics data‐sharing easy. Nat. Biotechnol. 27:598‐599.
   Côté, R., Jones, P., Martens, L., Kerrien, S., Reisinger, F., Lin, Q., Leinonen, R., Apweiler, R., and Hermjakob, H. 2007. The Protein Identifier Cross‐Referencing (PICR) service: Reconciling protein identifiers across multiple source databases. BMC Bioinformatics 8:401.
   Côté, R.G., Jones, P., Martens, L., Apweiler, R., and Hermjakob, H. 2008. The Ontology Lookup Service: More data and better tools for controlled vocabulary queries. Nucleic Acids Res. 36:W372‐W376.
   Editors. 2007. Democratizing proteomics data. Nat. Biotechnol. 25:262.
   Editors. 2008. Thou shalt share your data. Nat. Methods 5:209.
   Gevaert, K., Goethals, M., Martens, L., Van Damme, J., Staes, A., Thomas, G.R., and Vandekerckhove, J. 2003. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N‐terminal peptides. Nat. Biotechnol. 21:566‐569.
   Ghesquiere, B., Van Damme, J., Martens, L., Vandekerckhove, J., and Gevaert, K. 2006. Proteome‐wide characterization of N‐glycosylation events by diagonal chromatography. J. Proteome Res. 5:2438‐2447.
   Hubbard, T.J., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., Coates, G., Fairley, S., Fitzgerald, S., Fernandez‐Banet, J., Gordon, L., Graf, S., Haider, S., Hammond, M., Holland, R., Howe, K., Jenkinson, A., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Rios, D., Schuster, M., Slater, G., Smedley, D., Spooner, W., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, S., Zadissa, A., Birney, E., Cunningham, F., Curwen, V., Durbin, R., Fernandez‐Suarez, X.M., Herrero, J., Kasprzyk, A., Proctor, G., Smith, J., Searle, S., and Flicek, P. 2009. Ensembl 2009. Nucleic Acids Res. 37:D690‐D697.
   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.
   Jones, P., Côté, R.G., Cho, S.Y., Klie, S., Martens, L., Quinn, A.F., Thorneycroft, D., and Hermjakob, H. 2008. PRIDE: New developments and new datasets. Nucleic Acids Res. 36:D878‐D883.
   Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., and Apweiler, R. 2005a. PRIDE: The proteomics identifications database. Proteomics 5:3537‐3545.
   Martens, L., Vandekerckhove, J., and Gevaert, K. 2005b. DBToolkit: Processing protein databases for peptide‐centric proteomics. Bioinformatics 21:3584‐3585.
   Martens, L., Jones, P., and Côté, R. 2008. Using the Proteomics Identifications Database (PRIDE). Curr. Protoc. Bioinform. 21:13.8.1‐13.8.19.
   Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., Kanapin, A., Lewis, S., Mahajan, S., May, B., Schmidt, E., Vastrik, I., Wu, G., Birney, E., Stein, L., and D'Eustachio, P. 2009. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37:D619‐D622.
   Smedley, D., Haider, S., Ballester, B., Holland, R., London, D., Thorisson, G., and Kasprzyk, A. 2009. BioMart—Biological queries made easy. BMC Genomics 10:22.
   UniProt Consortium. 2009. The Universal Protein Resource (UniProt). 2009. Nucleic Acids Res. 37:D169‐D174.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library