Functional Proteomics

Methods and Protocols

  • Julie D. Thompson
  • Marius Ueffing
  • Christine Schaeffer-Reiss

Part of the Methods in Molecular Biology book series (MIMB, volume 484)

Table of contents

  1. Front Matter
    Pages i-xvii
  2. Introduction

  3. Proteomics

    1. Front Matter
      Pages 27-27
    2. Eric Sarnighausen, Ralf Reski
      Pages 29-44
    3. Lynne Thadikkaran, Nathalie Rufer, Corinne Benay, David Crettaz, Jean-Daniel Tissot
      Pages 45-65
    4. Natalia Govorukhina, Peter Horvatovich, Rainer Bischoff
      Pages 67-77
    5. Monique P. Gelderman, Jan Simak
      Pages 79-93
  4. Protein Expression Profiling

    1. Front Matter
      Pages 95-95
    2. Joost P. J. J. Hegmans, Peter J. Gerber, Bart N. Lambrecht
      Pages 97-109
    3. Sandrine Uttenweiler-Joseph, Stéphane Claverol, Loïk Sylvius, Marie-Pierre Bousquet-Dubouch, Odile Burlet-Schiltz, Bernard Monsarrat
      Pages 111-130
    4. Mikkel Nissum, Robert Wildgruber
      Pages 131-144
    5. Alex von Kriegsheim, Christian Preisinger, Walter Kolch
      Pages 177-192
    6. Mingyue He, Michael J. Taussig
      Pages 193-205
    7. Mingyue He, Michael J. Taussig
      Pages 207-215
    8. Petra Van Damme, Francis Impens, Joël Vandekerckhove, Kris Gevaert
      Pages 245-262
    9. David S. Selby, Martin R. Larsen, Cosima Damiana Calvano, Ole Nørregaard Jensen
      Pages 263-276
  5. Protein Analysis

    1. Front Matter
      Pages 277-277
    2. Lennart Martens, Luisa Montecchi Palazzi, Henning Hermjakob
      Pages 279-286
    3. Andrew Chatr-aryamontri, Andreas Zanzoni, Arnaud Ceol, Gianni Cesareni
      Pages 305-317
    4. Jennifer A. Siepen, Julian N. Selley, Simon J. Hubbard
      Pages 319-332
    5. Ingvar Eidhammer, Harald Barsnes, Svein-Ole Mikalsen
      Pages 345-359
    6. Frédéric Plewniak
      Pages 361-378
    7. Chuong B. Do, Kazutaka Katoh
      Pages 379-413
    8. Jasmin Šarić, Henriette Engelken, Uwe Reyle
      Pages 415-433
    9. Raja Mazumder, Sona Vasudevan, Anastasia N. Nikolskaya
      Pages 465-490
    10. Philip Wong, Dmitrij Frishman
      Pages 491-504
    11. Ozlem Keskin, Ruth Nussinov, Attila Gursoy
      Pages 505-521
    12. Florencio Pazos, David Juan, Jose M. G. Izarzugaza, Eduardo Leon, Alfonso Valencia
      Pages 523-535
    13. Antoine Coulon, Guillaume Beslon, Olivier Gandrillon
      Pages 537-558
  6. Back Matter
    Pages 579-599

About this book


As the emerging field of proteomics continues to expand at an extremely rapid rate, the relative quantification of proteins, targeted by their function, becomes its greatest challenge. Complex analytical strategies have been designed that allow comparative analysis of large proteomes, as well as in depth detection of the core proteome or the interaction network of a given protein of interest. In Functional Proteomics: Methods and Protocols, expert researchers describe the latest protocols being developed to address the problems encountered in high-throughput proteomics projects, with emphasis on the factors governing the technical choices for given applications. The case studies within the volume focus on the following three crucial aspects of the experimental design: 1) the strategy used for the selection, purification and preparation of the sample to be analyzed by mass spectrometry, 2) the type of mass spectrometer used and the type of data to be obtained from it, and 3) the method used for the interpretation of the mass spectrometry data and the search engine used for the identification of the proteins in the different types of sequence data banks available. As a part of the highly successful Methods in Molecular Biology™ series, the chapters compile step-by-step, readily reproducible laboratory protocols, lists of the necessary materials and reagents, and tips on troubleshooting and avoiding known pitfalls.

Comprehensive and cutting-edge, Functional Proteomics: Methods and Protocols is an ideal resource for all scientists pursuing this developing field and its multitudinous data.


Complex functional systems High-throughput proteomics Mass spectrometry Protein analysis Protein expression profiling Proteomics proteins

Editors and affiliations

  • Julie D. Thompson
    • 1
  • Marius Ueffing
    • 2
  • Christine Schaeffer-Reiss
    • 3
  1. 1.Laboratoire de Bioinformatique et Génomique IntégrativesInstitut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
  2. 2.Department of Protein Science Helmholtz Zentrum MünchenGerman Research Center for Environmental HealthMunich-NeuherbergGermany
  3. 3.LSMBO, ECPMInstitut Pluridisciplinaire Hubert CurienStrasbourgFrance

Bibliographic information

  • DOI
  • Copyright Information Humana Press 2008
  • Publisher Name Humana Press
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-58829-971-0
  • Online ISBN 978-1-59745-398-1
  • Series Print ISSN 1064-3745
  • Buy this book on publisher's site