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Life Sciences - Biochemistry & Biophysics | Functional Proteomics - Methods and Protocols

Functional Proteomics

Methods and Protocols

Series: Methods in Molecular Biology, Vol. 484

Thompson, Julie D., Schaeffer-Reiss, Christine, Ueffing, Marius (Eds.)

2008

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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

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.

Content Level » Research

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

Related subjects » Analytical Chemistry - Biochemistry & Biophysics

Table of contents 

Preface Contributors Part I: Introduction 1. A Brief Summary of the Different Types of Mass Spectrometers Used in Proteomics Christine Schaeffer-Reiss 2. Experimental Setups and Considerations to Study Microbial Interactions Petter Melin Part II: Proteomics 3. Plant Proteomics Eric Sarnighausen and Ralf Reski 4. Methods for Human CD8+ T Lymphocyte Proteome Analysis Lynne Thadikkaran, Nathalie Rufer, Corinne Benay, David Crettaz, and Jean-Daniel Tissot 5. Label-Free Proteomics of Serum Natalia Govorukhina, Peter Horvatovich, and Rainer Bischoff 6. Flow Cytometric Analysis of Cell Membrane Microparticles Monique P. Gelderman and Jan Simak Part III: Protein Expression Profiling 7. Exosomes Joost P. J. J. Hegmans, Peter J. Gerber, and Bart N. Lambrecht 8. 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 9. Free-Flow Electrophoresis of the Human Urinary Proteome Mikkel Nissum and Robert Wildgruber 10. Versatile Screening for Binary Protein–Protein Interactions by Yeast Two-Hybrid Mating Stef J. F. Letteboer and Ronald Roepman 11. 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 12. Mapping of Signaling Pathways by Functional Interaction Proteomics Alex von Kriegsheim, Christian Preisinger,and Walter Kolch 13. Selection of Recombinant Antibodies by Eukaryotic Ribosome Display Mingyue He and Michael J. Taussig 14. Production of Protein Arrays by Cell-Free Systems Mingyue He and Michael J. Taussig 15. Nondenaturing Mass Spectrometry to Study Noncovalent Protein/Protein and Protein/Ligand Complexes: Technical Aspects and Application to the Determination of Binding Stoichiometries Sarah Sanglier, C´edric Atmanene, Guillaume Chevreux, and Alain Van Dorsselaer 16. Protein Processing Characterized by a Gel-Free Proteomics Approach Petra Van Damme, Francis Impens, Joël Vandekerckhove, and Kris Gevaert 17. Identification and Characterization of N-Glycosylated Proteins Using Proteomics David S. Selby, Martin R. Larsen, Cosima Damiana Calvano, and Ole Nørregaard Jensen Part IV: Protein Analysis 18. Data Standards and Controlled Vocabularies for Proteomics Lennart Martens, Luisa Montecchi Palazzi, and Henning Hermjakob 19. The PRIDE Proteomics Identifications Database: Data Submission, Query, and Dataset Comparison Philip Jones and Richard Côté 20. Searching the Protein Interaction Space through the MINT Database Andreas Zanzoni, Andrew Chatr-aryamontri, Arnaud Ceol, and Gianni Cesareni 21. PepSeeker: Mining Information from Proteomic Data Jennifer A. Siepen, Julian N. Selley, and Simon J. Hubbard 22. Toward High-Throughput and Reliable Peptide Identification via MS/MS Spectra Jian Liu 23. MassSorter: Peptide Mass Fingerprinting Data Analysis Ingvar Eidhammer, Harald Barsnes, and Svein-Ole Mikalsen 24. Database Similarity Searches Frédéric Plewniak 25. Protein Multiple Sequence Alignment Chuong B. Do and Kazutaka

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