UNIT 13.14 Predicting Peptide Retention Times for Proteomics

  1. Oleg V. Krokhin1,
  2. Vic Spicer2

Published Online: 1 SEP 2010

DOI: 10.1002/0471250953.bi1314s31

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Krokhin, O. V. and Spicer, V. 2010. Predicting Peptide Retention Times for Proteomics. Current Protocols in Bioinformatics. 31:13.14:13.14.1–13.14.15.

Author Information

  1. 1

    Department of Internal Medicine, University of Manitoba, Winnipeg, Canada

  2. 2

    Department of Physics and Astronomy, University of Manitoba, Winnipeg, Canada

Publication History

  1. Published Online: 1 SEP 2010
  2. Published Print: SEP 2010


The vast majority of modern bottom-up proteomic protocols include chromatographic reversed-phase (RP) fractionation of peptides prior to mass-spectrometric analysis. Retention time information can be easily extracted from LC-MS data and it can be used to improve protein identification/characterization procedures. The key to the success of this procedure is the correct retention time prediction based on compositional and structural properties of the separated species. Our Sequence Specific Retention Calculator (SSRCalc) is a Web-based peptide retention prediction that covers the separation selectivity of the most popular RP-HPLC conditions applied in proteomics. Procedures for the application of SSRCalc to proteomic analyses are described in this unit. Curr. Protoc. Bioinform. 31:13.14.1-13.14.15. © 2010 by John Wiley & Sons, Inc.


  • peptide retention prediction;
  • reversed-phase HPLC;
  • protein identification