UNIT 13.3 Protein Identification Using TurboSEQUEST

  1. Deborah H. Lundgren1,
  2. David K. Han1,
  3. Jimmy K. Eng2

Published Online: 1 JUL 2005

DOI: 10.1002/0471250953.bi1303s10

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Lundgren, D. H., Han, D. K. and Eng, J. K. 2005. Protein Identification Using TurboSEQUEST. Current Protocols in Bioinformatics. 10:13.3:13.3.1–13.3.13.

Author Information

  1. 1

    University of Connecticut Health Center, Farmington, Connecticut

  2. 2

    Fred Hutchinson Cancer Research Center, Seattle, Washington

Publication History

  1. Published Online: 1 JUL 2005
  2. Published Print: JUN 2005

This is not the most recent version of the article. View current version (1 DEC 2009)


SEQUEST is the most widely used software tool for identifying proteins in complex mixtures. It is a mature, robust program that identifies peptides directly from uninterpreted tandem mass spectra, thus making large-scale proteomic studies possible. Thermo Electron's TurboSEQUEST provides a Windows-based graphical user interface for running SEQUEST and interpreting results. The protocol in this unit describes the basic steps involved in processing mass spectrometric data and analyzing results using TurboSEQUEST. It also provides an overview of the SEQUEST algorithm and a discussion of data filtering methods, critical issues in data interpretation, and available resources that can facilitate proper interpretation of SEQUEST results.


  • bioinformatics;
  • CID;
  • MS/MS;
  • peptide ion fragmentation;
  • posttranslational modifications;
  • protein identification;
  • proteomics;
  • tandem mass spectrometry