Standard Article

Tandem mass spectrometry database searching

Part 3. Proteomics

3.1. Core Methodologies

Specialist Review

  1. Jimmy K. Eng,
  2. Daniel B. Martin,
  3. Ruedi Aebersold

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g301204

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Eng, J. K., Martin, D. B. and Aebersold, R. 2005. Tandem mass spectrometry database searching. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.1:3.

Author Information

  1. Institute for Systems Biology, Seattle, WA, USA

Publication History

  1. Published Online: 15 APR 2005

Abstract

Associated with the emergence of mass spectrometry–based proteomics analysis, a host of novel algorithms for tandem mass spectrometry database searching have been published. These tools apply a breadth of computational and statistical approaches to solving the problem of identifying peptides based on interpreting tandem mass spectra with the constraint of sequences present in publicly available protein, transcript, and genomic sequence database repositories. With increasing data volumes due to continuous advances in instrumentation, the need for tools that perform automated peptide identifications and validation of those identifications will be magnified. An overview of database search and postsearch validation tools is summarized.

Keywords:

  • database searching;
  • peptide fingerprinting;
  • tandem mass spectrometry;
  • proteomics;
  • bioinformatics