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Improvement of sequence coverage in peptide mass fingerprinting

Part 3. Proteomics

3.1. Core Methodologies

Basic Techniques and Approaches

  1. Karin Hjernø,
  2. Peter Roepstorff

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g301413

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Hjernø, K. and Roepstorff, P. 2005. Improvement of sequence coverage in peptide mass fingerprinting. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.1:16.

Author Information

  1. University of Southern Denmark, Odense, Denmark

Publication History

  1. Published Online: 15 APR 2005

Abstract

In order to fully characterize and understand the biological significance of a protein (in a proteomics study), it needs to be characterized with respect to the presence of splice variants, isoforms, and posttranslational processing/modification. This requires full coverage of the protein sequence including that of minor variants of the protein. However, protein identification is often based on sequence coverages as low as 10–20%, and search for the remaining peptides is frequently like the search for the needle in the haystack. Here we present some approaches, which may be helpful for increasing the sequence coverage in proteomics studies.

Keywords:

  • peptide mass fingerprinting;
  • sequence coverage;
  • multiple enzymatic digestion;
  • ion suppression;
  • MALDI;
  • ESI;
  • LCMS;
  • graphite microcolumn