Functional proteomics : methods and protocols / edited by Julie D. Thompson, Christine Schaeffer-Reiss, Marius Ueffing.

Format:

Book

Contributor:

Thompson, Julie D.

Schaeffer-Reiss, Christine.

Ueffing, Marius.

Series:

Methods in molecular biology (Clifton, N.J.) ; 484.

Methods in molecular biology, 1064-3745 ; 484

Language:

English

Subjects (All):

Proteomics.

Proteomics--methods.

Medical Subjects:

Proteomics--methods.

Physical Description:

xvii, 595 pages, 4 unnumbered pages of plates : illustrations (some color) ; 25 cm.

Place of Publication:

Totowa, NJ : Humana Press, [2008]

Summary:

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.

Contents:

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

Plant proteomics / Eric Sarnighausen and Ralf Reski

Methods for human CD8+ T lymphocyte proteome analysis / Lynne Thadikkaran ... [et al.]

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

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 ... [et al.]

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 : technical aspects and application to the determination of binding stoichiometries / Sarah Sanglier ... [et al.]

Protein processing characterized by a gel-free proteomics approach / Petra Van Damme ... [et al.]

Identification and characterization of N-glycosylated proteins using proteomics / David S. Selby ... [et al.]

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 / Andrew Chatr-aryamontri ... [et al.]

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 Šaríc, 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 ... [et al.]

Large multiprotein structures 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.

Notes:

"Springer protocols"--Cover.

Includes bibliographical references and index.

ISBN:

9781588299710

1588299716

OCLC:

227033904