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Protein fingerprinting

Part 3. Proteomics

3.1. Core Methodologies

Short Specialist Review

  1. David Fenyo

Published Online: 15 NOV 2005

DOI: 10.1002/047001153X.g301306

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Fenyo, D. 2005. Protein fingerprinting. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.1:12.

Author Information

  1. GE Healthcare, Piscataway, NJ, USA

Publication History

  1. Published Online: 15 NOV 2005

Abstract

Peptide mass fingerprinting is a technique that is widely used to identify individual proteins of interest in proteomic projects. This method depends on the in silico comparison of an experimental mass spectrum (“mass fingerprint”) of the protein of interest with calculated peptide masses from a protein sequence collection. A variety of search engines (e.g., Mascot, ProFound, and MS-Fit) are available for such analysis and the output consists of a list of potential protein identities ranked according to their score values. The meaning of these scores is in general not easily understood by the nonexpert user and they are not amenable to automation. Therefore, an additional step is necessary to test the significance of the results and convert the search engine–dependent score into a measurement of the significance of the protein identification result. This paper discusses how different search parameters influence the results and how the search engine–dependent scores can be converted into a measurement of the significance of the protein identification result.

Keywords:

  • database search algorithms;
  • enzymatic digestion;
  • mass spectrometry;
  • peptide mass fingerprinting;
  • protein identification;
  • protein modifications;
  • significance testing