UNIT 25.2 Overview of Tandem Mass Spectrometry (MS/MS) Database Search Algorithms

  1. Eugene Kapp1,
  2. Frédéric Schütz2

Published Online: 1 AUG 2007

DOI: 10.1002/0471140864.ps2502s49

Current Protocols in Protein Science

Current Protocols in Protein Science

How to Cite

Kapp, E. and Schütz, F. 2007. Overview of Tandem Mass Spectrometry (MS/MS) Database Search Algorithms. Current Protocols in Protein Science. 49:25.2:25.2.1–25.2.19.

Author Information

  1. 1

    Ludwig Institute for Cancer Research, Melbourne, Australia

  2. 2

    Swiss Institute of Bioinformatics, Lausanne, Switzerland

Publication History

  1. Published Online: 1 AUG 2007
  2. Published Print: AUG 2007


Mass spectrometry–based methods for the identification of proteins are fundamental platform technologies for proteomics. One comprehensive approach is to subject trypsinized peptides to tandem mass spectrometry (MS/MS) to obtain detailed structural information. Different strategies are available for interpreting MS/MS data and hence deducing the amino acid sequence of the peptides. The most common method is to use a search algorithm to identify peptides by correlating experimental and theoretical MS/MS data (the latter being generated from possible peptides in the protein sequence database). Identified peptides are collated and protein entries from the sequence database inferred. This unit focuses on the most widely used tandem MS peptide identification search algorithms (commercial and open source), their availability, ease of use, strengths, speed and scoring, as well as their relative sensitivity and specificity. Curr. Protoc. Protein Sci. 49:25.2.1-25.2.19. © 2007 by John Wiley & Sons, Inc.


  • Mascot;
  • X!Tandem;
  • OMSSA;
  • PLGS;
  • Sorcerer;
  • ProteinPilot;
  • Phenyx;
  • SpectrumMill