Main description:

A compendium of thirty-four powerful techniques for identifying and analyzing the diversity of proteins expressed in cells. Thee readily reproducible proteomic methods range from general to specific techniques, and include methods for data analysis, posttranslational modification, and its variants and isoforms. Additional methods demonstrate the application of proteomics to the discovery of serological tumor markers, to identifying the determinants of sensitivity to antitumor drugs, and to specialized fields, such as endocrinology, plant biology, nephrology, and urology.

Contents:

Part I. General Techniques

Proteomics and the Molecular Biologist
Paul R. Graves and Timothy A. J. Haystead

Protein Identification from 2-D Gels Using In Vitro Transcription Translation Products
Nathalie Norais, Renzo Nogarotto, Emilia Tiziana Iacobini, Ignazio Garaguso, Renata Grifantini, Giuliano Galli, and Guido Grandi

Selective Chemical Cleavage Methods in Proteomics, Including C-Terminal Successive Degradation
Akira Tsugita

Means of Hydrolyzing Proteins Isolated upon ProteinChip (R) Array Surfaces: Chemical and Enzymatic Approaches
Shanhua Lin, Ning Tang, and Scot R. Weinberger

A Combined Radiolabeling and Silver Staining Technique for Improved Visualization and Localization of Proteins on Two-Dimensional Gels
Jules A. Westbrook and Michael J. Dunn

Qualitative and Quantitative Proteomic Analyses via Multidimensional Protein Identification Technology
Michael P. Washburn and David M. Schieltz

Di- and Tri-Chromatic Fluorescence Detection on Western Blots
Karen J. Martin and Wayne F. Patton

Multiplexed Proteomics: Fluorescence Detection of Protein Differences by Two-Dimensional Gel Electrophoresis and Computer-Based Differential Display
Birte Schulenberg and Wayne F. Patton

A Strategy for Characterizing Antibody/Antigen Interactions Using ProteinChip (R) Arrays
Alexandra Huhalov, Daniel I. R. Spencer, and Kerry A. Chester

Stable Isotope Labeling with Amino Acids as an Aid to Protein Identification in Peptide Mass Fingerprinting
Robert J. Beynon

The Use of 18O Labeling as a Tool for Proteomic Applications
Ian I. Stewart, Ty Thomson, Daniel Figeys, and Henry S. Duewel

Automated Nanoflow Liquid Chromatography/Tandem Mass Spectrometric Identification of Liver Mitochondrial Proteins
Bart Devreese, Frank Vanrobaeys, Elke Lecocq, Joel Smet, Rudy Van Coster, and Jozef VanBeeumen

In Silico Proteomics: Predicting Interactions from Sequence
Joel R. Bock and David A. Gough

Part II. Post-Translational Modifications, Variants, and Isoforms

Predicting Glycan Composition from Experimental Mass Using GlycoMod
Catherine A. Cooper, Elisabeth Gasteiger, and Nicolle H. Packer

Querying GlycoSuiteDB
Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins, and Nicolle H. Packer

New Tools for Quantitative Phosphoproteome Analysis
Li-Rong Yu, Van M. Hoang, and Timothy D. Veenstra

Computer-Aided Strategies for Characterizing Protein Isoforms
Frederic Nikitin and Frederique Lisacek

Protein Variant Separations Using Cation Exchange Chromatography on Grafted, Polymeric Stationary Phases
Michael Weitzhandler, Dell Farnan, Nebojsa Avdalovic, and Chris Pohl

Part III. Specific Systems

Noninvasive Imaging of Protein-Protein Interactions in Living Animals
Gary D. Luker, Vijay Sharma, and David Piwnica-Worms

Strategies in Clinical Proteomics
Eric T. Fung

Proteomic Profiling of the Cancer Microenvironment
Vladimir Knezevic and Michael R. Emmert-Buck

Identification of Determinants of Sensitivity to Antitumor Drugs
Paola Perego, Giovanni Luca Beretta, and Laura Gatti

Application of Proteomics to the Discovery of Serological Tumor Markers
Terence C. W. Poon and Philip J. Johnson

Infectomic Analysis of Microbial Infections Using Proteomics
Sheng-He Huang, Ambrose Jong, and James T. Summersgill

Toward a Complete Proteome of Bacillus subtilis: Cytosolic, Cell Wall-Associated, and Extracellular Proteins
Haike Antelmann, Jan Maarten van Dijl, and Michael Hecker

Renal and Urinary Proteomics
Visith Thongboonkerd, Elias Klein, and Jon B. Klein

Proteomics in Endocrinology
Jan W. A. Smit and