Protocol

The Proteomics Protocols Handbook

pp 571-607

Protein Identification and Analysis Tools on the ExPASy Server

  • Elisabeth GasteigerAffiliated withSwiss Institute of Bioinformatics
  • , Christine HooglandAffiliated withSwiss Institute of Bioinformatics
  • , Alexandre GattikerAffiliated withSwiss Institute of Bioinformatics
  • , S'everine DuvaudAffiliated withSwiss Institute of Bioinformatics
  • , Marc R. WilkinsAffiliated withProteome Systems Ltd.
  • , Ron D. AppelAffiliated withSwiss Institute of Bioinformatics, University and Geneva University Hospital
  • , Amos BairochAffiliated withSwiss Institute of Bioinformatics

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Abstract

Protein identification and analysis software performs a central role in the investigation of proteins from two-dimensional (2-D) gels and mass spectrometry. For protein identification, the user matches certain empirically acquired information against a protein database to define a protein as already known or as novel. For protein analysis, information in protein databases can be used to predict certain properties about a protein, which can be useful for its empirical investigation. The two processes are thus complementary. Although there are numerous programs available for those applications, we have developed a set of original tools with a few main goals in mind. Specifically, these are:
  1. 1.

    To utilize the extensive annotation available in the Swiss-Prot database (1) wherever possible, in particular the position-specific annotation in the Swiss-Prot feature tables to take into account posttranslational modifications and protein processing.

     
  2. 2.

    To develop tools specifically, but not exclusively, applicable to proteins prepared by twodimensional gel electrophoresis and peptide mass fingerprinting experiments.

     
  3. 3.

    To make all tools available on the World-Wide Web (WWW), and freely usable by the scientific community.