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Functional Proteomics - Methods and Protocols

Edited by Thompson, Julie D.; Schaeffer-Reiss, Christine; Ueffing, Marius 
Springer  August 2008  



Hardcover  598 pp  ISBN 9781588299710      £117.00
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.

Written for researchers working in the field of proteomics including chemical engineers, analytical chemists, biochemists, cell and molecular biologists, clinical scientists and bioinformaticians, as well as those who are contemplating using proteomics for functional studies

Contents

Preface
Contributors

Part I: Introduction

  • A Brief Summary of the Different Types of Mass Spectrometers Used in Proteomics , Christine Schaeffer-Reiss
  • Experimental Setups and Considerations to Study Microbial Interactions , Petter Melin

Part II: Proteomics

  • Plant Proteomics, Eric Sarnighausen and Ralf Reski
  • Methods for Human CD8+ T Lymphocyte Proteome Analysis, Lynne Thadikkaran, Nathalie Rufer, Corinne Benay, David Crettaz, and Jean-Daniel Tissot
  • Label-Free Proteomics of Serum, Natalia Govorukhina, Peter Horvatovich, and Rainer Bischoff
  • Flow Cytometric Analysis of Cell Membrane Microparticles , Monique P. Gelderman and Jan Simak

Part III: Protein Expression Profiling

  • Exosomes, Joost P. J. J. Hegmans, Peter J. Gerber, and Bart N. Lambrecht
  • 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, and Bernard Monsarrat
  • Free-Flow Electrophoresis of the Human Urinary Proteome, Mikkel Nissum and Robert Wildgruber
  • Versatile Screening for Binary Protein-Protein Interactions by Yeast Two-Hybrid Mating, Stef J. F. Letteboer and Ronald Roepman
  • 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, and Marius Ueffing
  • Mapping of Signaling Pathways by Functional Interaction Proteomics, Alex von Kriegsheim, Christian Preisinger, and Walter Kolch
  • Selection of Recombinant Antibodies by Eukaryotic Ribosome Display, Mingyue He and Michael J. Taussig
  • Production of Protein Arrays by Cell-Free Systems, Mingyue He and Michael J. Taussig
  • Nondenaturing Mass Spectrometry to Study Noncovalent Protein/Protein and Protein/Ligand Complexes: Protein Processing Characterized by a Gel-Free Proteomics Approach, Petra Van Damme, Francis Impens, Joël Vandekerckhove, and Kris Gevaert
  • Identification and Characterization of N-Glycosylated Proteins Using Proteomics, David S. Selby, Martin R. Larsen, Cosima Damiana Calvano, and Ole Norregaard Jensen

Part IV: Protein Analysis

  • Data Standards and Controlled Vocabularies for Proteomics, Lennart Martens, Luisa Montecchi Palazzi, and Henning Hermjakob
  • The PRIDE Proteomics Identifications Database: Data Submission, Query, and Dataset Comparison, Philip Jones and Richard Côté
  • Searching the Protein Interaction Space through the MINT Database, Andreas Zanzoni, Andrew Chatr-aryamontri, Arnaud Ceol, and Gianni Cesareni
  • PepSeeker: Mining Information from Proteomic Data, Jennifer A. Siepen, Julian N. Selley, and Simon J. Hubbard
  • Toward High-Throughput and Reliable Peptide Identification via MS/MS Spectra, Jian Liu
  • MassSorter: Peptide Mass Fingerprinting Data Analysis, Ingvar Eidhammer, Harald Barsnes, and Svein-Ole Mikalsen
  • Database Similarity Searches , Frédéric Plewniak
  • Protein Multiple Sequence Alignment , Chuong B. Do and Kazutaka Katoh
  • Discovering Biomedical Knowledge from the Literature, Jasmin Saric, Henriette Engelken, and Uwe Reyle
  • Protein Subcellular Localization Prediction Using Artificial Intelligence Technology, Rajesh Nair and Burkhard Rost
  • Protein Functional Annotation by Homology, Raja Mazumder, Sona Vasudevan, and Anastasia N. Nikolskaya
  • Designability and Disease, Philip Wong and Dmitrij Frishman
  • Prism: Protein-Protein Interaction Prediction by Structural Matching, Ozlem Keskin, Ruth Nussinov, and Attila Gursoy
  • Prediction of Protein Interaction Based on Similarity of Phylogenetic Trees, Florencio Pazos, David Juan, Jose M. G. Izarzugaza, Eduardo Leon, and Alfonso Valencia
  • Large Multiprotein Structure Modeling and Simulation: The Need for Mesoscopic Models, Antoine Coulon, Guillaume Beslon, and Olivier Gandrillon
  • Dynamic Pathway Modeling of Signal Transduction Networks: A Domain-Oriented Approach, Holger Conzelmann and Ernst-Dieter Gilles
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Springer : biotechnology : methods : proteins : proteomics : protocols

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