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Tutorial on tandem mass spectrometry database searching

Part 3. Proteomics

3.1. Core Methodologies

Basic Techniques and Approaches

  1. Jimmy K. Eng

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g301405

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Eng, J. K. 2005. Tutorial on tandem mass spectrometry database searching. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.1:17.

Author Information

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

Publication History

  1. Published Online: 15 APR 2005

Abstract

Identifying peptides, and ultimately proteins, by searching sequence databases with tandem mass spectra of peptides is one of the most widely used proteomics techniques. The steps by which a user actually performs a search are fairly straightforward and are described in this article. Although this article goes through the identification process of searching a single tandem mass spectrum to identify a single peptide, most users will not usually selective search only one spectrum but would query the full set of tandem mass spectra acquired in an entire LC-MS/MS run. The underlying steps and analysis considerations outlined here are relevant in either scenario.

Keywords:

  • database searching;
  • peptide fingerprinting;
  • tandem mass spectrometry;
  • MS/MS;
  • proteomics;
  • tutorial