Chapter II-4. Proteome Analysis

  1. Prof. Dr. Thomas Lengauer Ph.D.
  1. Dr. Pierre-Alain Binz1,
  2. Dr. Elisabeth Gasteiger2,
  3. Dr. Jean-Charles Sanchez3,
  4. Dr. Amos Bairoch2,
  5. Prof. Dr. Denis F. Hochstrasser3 and
  6. Prof. Ron D. Appel1

Published Online: 1 APR 2004

DOI: 10.1002/3527601481.ch12

Bioinformatics - From Genomes to Drugs

Bioinformatics - From Genomes to Drugs

How to Cite

Binz, P.-A., Gasteiger, E., Sanchez, J.-C., Bairoch, A., Hochstrasser, D. F. and Appel, R. D. (2001) Proteome Analysis, in Bioinformatics - From Genomes to Drugs (ed T. Lengauer), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527601481.ch12

Editor Information

  1. Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany

Author Information

  1. 1

    Swiss Institute of Bioinformatics, Proteome Informatics group, CMU-1, rue Michel Servet, 1211 Geneva 4, Switzerland

  2. 2

    Swiss Institute of Bioinformatics, SWISS-PROT group, CMU-1, rue Michel Servet, 1211 Geneva 4, Switzerland

  3. 3

    Laboratoire Central de Chimie Clinique, Hôpital Cantonal Universitaire, 24, rue Micheli-du-Crest, 1211 Genève 14, Switzerland

Publication History

  1. Published Online: 1 APR 2004
  2. Published Print: 1 NOV 2001

Book Series:

  1. Methods and Principles in Medicinal Chemistry

Book Series Editors:

  1. Prof. Dr. Raimund Mannhold5,
  2. Prof. Dr. Hugo Kubinyi6 and
  3. Prof. Dr. Gerd Folkers7

Series Editor Information

  1. 5

    Biomedical Research Center, Molecular Drug Research Group, Heinrich-Heine-Universität, Universitätsstraße 1, D-40225 Düsseldorf, Germany

  2. 6

    BASF AG, Ludwigshaften, c/o Donnersbergstrasse g, D-67256 Weisenheim am Sand, Germany

  3. 7

    Department of Applied Biosciences, ETH Zürich, Winterthurer Str. 190, CH-8057 Zürich, Switzerland

ISBN Information

Print ISBN: 9783527299881

Online ISBN: 9783527601486



  • proteome;
  • protein separation;
  • 2-DE technology;
  • 2-DE gel images;
  • proteome databases;
  • interPro;
  • peptide mass fingerprinting;
  • molecular scanner


This chapter contains sections titled:

  • Introduction and principles

  • Protein separation

    • Experimental aspects: description of the 2-DE technology, a wet-lab technique, from a wet-lab point of view

    • The use of 2-DE as a tool towards diagnostics and disease description

  • Computer analysis of 2-DE gel images

    • 2-DE analysis software

  • Identification and characterization of proteins after separation

    • Introduction

    • The tools

  • Proteome databases

    • Introduction

    • Protein sequence databases

    • Nucleotide sequence databases

    • Databases for protein families, domains and functional sites: InterPro

    • 2-DE databases

    • Post-translational modification databases

    • Conclusion

  • Automation in proteome analysis

    • Introduction

    • Robotized protein identification using peptide mass fingerprinting

    • The molecular scanner

    • Other techniques

  • Conclusion