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The PROTICdb Database for 2-DE Proteomics

  • Olivier Langella
  • Michel Zivy
  • Johann Joets
Part of the Methods in Molecular Biology book series (MIMB, volume 355)

Abstract

PROTICdb is a web-based database mainly designed to store and analyze plant proteome data obtained by 2D polyacrylamide gel electrophoresis (2D PAGE) and mass spectrometry (MS). The goals of PROTICdb are (1) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements; and (2) to integrate information from the user’s own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of posttranslational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs from Mélanie, PDQuest, IM2d, ImageMaster(tm) 2D Platinum v5.0, Progenesis, Sequest, MS-Fit, and Mascot software, or by filling in web forms (experimental design and methods). 2D PAGE-annotated maps can be displayed, queried, and compared through the GelBrowser. Quantitative data can be easily exported in a tabulated format for statistical analyses with any third-party software. PROTICdb is based on the Oracle or the PostgreSQLDataBase Management System (DBMS) and is freely available upon request at http://cms.moulon.inra.fr/content/view/14/44/.

Key Words

Database comparative proteomics mass spectrometry two-dimensional polyacrylamide gel electrophoresis Gene Ontology 

References

  1. 1.
    Görg, A., Weiss, and Dunn M. J. (2004) Current two-dimensional electrophoresis technology for proteomics. Proteomics 4, 3665–4036.CrossRefPubMedGoogle Scholar
  2. 2.
    Canovas, F. M., Dumas-Gaudot, E., Recorbet, G., Jorrin, J., Mock H. P., and Rossignol M. (2004) Plant proteome analysis. Proteomics 4, 285–298.CrossRefPubMedGoogle Scholar
  3. 3.
    Zhu, H., Bilgin, M., and Snyder M. (2003) Proteomics. Annu. Rev. Biochem. 72, 783–812.CrossRefPubMedGoogle Scholar
  4. 4.
    Pandey, A. and Mann, M. (2000) proteomics to study genes and genomes. Nature 405, 837–846.CrossRefPubMedGoogle Scholar
  5. 5.
    Ferry-Dumazet H., Houel G., Montalent P., et al. (2005) PROTICdb: a web-based application to store, track, query and compare plant proteome data Proteomics 5, 2069–2081.CrossRefPubMedGoogle Scholar
  6. 6.
    Harris M. A., Clark J., Ireland A., et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 132, D258–D261.Google Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Olivier Langella
    • 1
  • Michel Zivy
    • 1
  • Johann Joets
    • 1
  1. 1.UMR de Génétique Végétale, La Ferme du MoulonGif-sur-YvetteFrance

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