Functional Proteomics: Methods and Protocols

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August 2008



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(TM) 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.



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


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)
EAN: 9781588299710
ISBN: 1588299716
Untertitel: 'Methods in Molecular Biology'. Sprache: Englisch.
Erscheinungsdatum: August 2008
Seitenanzahl: 595 Seiten
Format: gebunden
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