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Functional Proteomics

Methods and Protocols

  • Book
  • © 2008

Overview

Editors:
  1. Julie D. Thompson

    1. Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France

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  2. Marius Ueffing

    1. Department of Protein Science Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany

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  3. Christine Schaeffer-Reiss

    1. LSMBO, ECPM, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France

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  • Unique combination of reproducible laboratory protocols and state-of-the-art bioinformatics methods dedicated to functional proteomics
  • A comprehensive methodological compendium, covering sample preparation, protein separation, mass-spectrometry as well as data mining, documentation and integration
  • Offers methods, workflows and strategies to overcome current pitfalls and shortcomings in proteome analysis

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

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Table of contents (33 protocols)

  1. Front Matter

    Pages i-xvii
    Download chapter PDF

  3. Proteomics

    1. Front Matter

      Pages 27-27
      Download chapter PDF

    2. Plant Proteomics

      • Eric Sarnighausen, Ralf Reski
      Pages 29-44

    3. Methods for Human CD8+ T Lymphocyte Proteome Analysis

      • Lynne Thadikkaran, Nathalie Rufer, Corinne Benay, David Crettaz, Jean-Daniel Tissot
      Pages 45-65

    4. Label-Free Proteomics of Serum

      • Natalia Govorukhina, Peter Horvatovich, Rainer Bischoff
      Pages 67-77

    5. Flow Cytometric Analysis of Cell Membrane Microparticles

      • Monique P. Gelderman, Jan Simak
      Pages 79-93

  4. Protein Expression Profiling

    1. Front Matter

      Pages 95-95
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    2. Exosomes

      • Joost P. J. J. Hegmans, Peter J. Gerber, Bart N. Lambrecht
      Pages 97-109

    3. Toward a Full Characterization of the Human 20S Proteasome Subunits and Their Isoforms by a Combination of Proteomic Approaches

      • Sandrine Uttenweiler-Joseph, Stéphane Claverol, Loïk Sylvius, Marie-Pierre Bousquet-Dubouch, Odile Burlet-Schiltz, Bernard Monsarrat
      Pages 111-130

    4. Free-Flow Electrophoresis of the Human Urinary Proteome

      • Mikkel Nissum, Robert Wildgruber
      Pages 131-144

    5. Versatile Screening for Binary Protein-Protein Interactions by Yeast Two-Hybrid Mating

      • Stef J. F. Letteboer, Ronald Roepman
      Pages 145-159

    6. Native Fractionation: Isolation of Native Membrane-Bound Protein Complexes from Porcine Rod Outer Segments Using Isopycnic Density Gradient Centrifugation

      • Magdalena Swiatek-de Lange, Bernd Müller, Marius Ueffing
      Pages 161-175

    7. Mapping of Signaling Pathways by Functional Interaction Proteomics

      • Alex von Kriegsheim, Christian Preisinger, Walter Kolch
      Pages 177-192

    8. Selection of Recombinant Antibodies by Eukaryotic Ribosome Display

      • Mingyue He, Michael J. Taussig
      Pages 193-205

    9. Production of Protein Arrays by Cell-Free Systems

      • Mingyue He, Michael J. Taussig
      Pages 207-215

    10. Nondenaturing Mass Spectrometry to Study Noncovalent Protein/Protein and Protein/Ligand Complexes: Technical Aspects and Application to the Determination of Binding Stoichiometries

      • Sarah Sanglier, Cédric Atmanene, Guillaume Chevreux, Alain Van Dorsselaer
      Pages 217-243

    11. Protein Processing Characterized by a Gel-Free Proteomics Approach

      • Petra Van Damme, Francis Impens, Joël Vandekerckhove, Kris Gevaert
      Pages 245-262
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Keywords

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.

Reviews

From the reviews: “The new book, Functional Proteomics, Methods and Protocols … is the perfect guide to securely navigating through the plethora of recent as well as established proteomic technologies. … In summary, I highly recommend this book as an excellent source for gaining insight into a diverse array of the latest proteomic protocols … . suitable for everyone working in the field of proteomics, including chemists, biologists, analytical chemists, and biochemists at different career stages, from students to the trained and experienced scientist.” (Stephan A. Sieber, ChemBioChem, Vol. 10 (18), 2009) “Book presents a collection of methods about correct techniques to identify, monitor, quantify, and explain protein and peptide function. … present different types of mass spectrometers and their uses, allowing the reader to choose the most useful technique for a specific purpose. … The strategy behind metabolomic studies is well described in this book. … The book concludes with the indispensable application of bioinformatics in the understanding of regulatory and protein systems which are influenced by the environment.” (Mario Hiroyuki Hirata, Brazilian Journal of Pharmaceutical Sciences, 2010) “The field of proteomics continues to develop rapidly and its main focus has now moved from increasing capacity for protein identification to quantification and the analysis of post-translational modifications. … this volume attempts to provide detail regarding some of the latest approaches being used. … will be of use to many PhD students and postdoctoral scientists … . a well-written and informative book, and one which would be useful to have in any proteomics lab … .” (Lucas Bowler, Microbiology Today, August, 2010)

Editors and Affiliations

  • Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France

    Julie D. Thompson

  • Department of Protein Science Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany

    Marius Ueffing

  • LSMBO, ECPM, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France

    Christine Schaeffer-Reiss

Bibliographic Information

  • Book Title: Functional Proteomics

  • Book Subtitle: Methods and Protocols

  • Editors: Julie D. Thompson, Marius Ueffing, Christine Schaeffer-Reiss

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-398-1

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2008

  • Hardcover ISBN: 978-1-58829-971-0Published: 12 August 2008

  • Softcover ISBN: 978-1-61737-860-7Published: 16 December 2010

  • eBook ISBN: 978-1-59745-398-1Published: 01 July 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVIII, 596

  • Number of Illustrations: 111 b/w illustrations, 4 illustrations in colour

  • Topics: Biochemistry, general, Protein Science, Proteomics, Mass Spectrometry

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