UNIT 13.3 Protein Identification Using Sorcerer 2 and SEQUEST

  1. Deborah H. Lundgren1,
  2. Harryl Martinez2,
  3. Michael E. Wright2,
  4. David K. Han1

Published Online: 1 DEC 2009

DOI: 10.1002/0471250953.bi1303s28

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Lundgren, D. H., Martinez, H., Wright, M. E. and Han, D. K. 2009. Protein Identification Using Sorcerer 2 and SEQUEST. Current Protocols in Bioinformatics. 28:13.3:13.3.1–13.3.21.

Author Information

  1. 1

    Department of Cell Biology, Center for Vascular Biology, University of Connecticut Health Center, Farmington, Connecticut

  2. 2

    Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, Iowa

Publication History

  1. Published Online: 1 DEC 2009
  2. Published Print: DEC 2009


Sage-N's Sorcerer 2 provides an integrated data analysis system for comprehensive protein identification and characterization. It runs on a proprietary version of SEQUESTR, the most widely used search engine for identifying proteins in complex mixtures. The protocol presented here describes the basic steps performed to process mass spectrometric data with Sorcerer 2 and how to analyze results using TPP and Scaffold. The unit also provides an overview of the SEQUESTR algorithm, along with Sorcerer-SEQUESTR enhancements, and a discussion of data filtering methods, important considerations in data interpretation, and additional resources that can be of assistance to users running Sorcerer and interpreting SEQUESTR results. Curr. Protoc. Bioinform. 28:13.3.1-13.3.21. © 2009 by John Wiley & Sons, Inc.


  • Sorcerer;
  • Scaffold;
  • Ascore;
  • TPP;
  • proteomics;
  • post-translational modifications;
  • false discovery rate;
  • quantification