Part I. General Techniquesn n Proteomics and the Molecular Biologistn Paul R. Graves and Timothy A. J. Haysteadn n Protein Identification from 2-D Gels Using In Vitro Transcription Translation Productsn Nathalie Norais, Renzo Nogarotto, Emilia Tiziana Iacobini, Ignazio Garaguso, Renata Grifantini, Giuliano Galli, and Guido Grandin n Selective Chemical Cleavage Methods in Proteomics, Including C-Terminal Successive Degradationn Akira Tsugitan n Means of Hydrolyzing Proteins Isolated upon ProteinChip® Array Surfaces: Chemical and Enzymatic Approachesn Shanhua Lin, Ning Tang, and Scot R. Weinbergern n A Combined Radiolabeling and Silver Staining Technique for Improved Visualization and Localization of Proteins on Two-Dimensional Gelsn Jules A. Westbrook and Michael J. Dunnn n Qualitative and Quantitative Proteomic Analyses via Multidimensional Protein Identification Technologyn Michael P. Washburn and David M. Schieltzn n Di- and Tri-Chromatic Fluorescence Detection on Western Blotsn Karen J. Martin and Wayne F. Pattonn n Multiplexed Proteomics: Fluorescence Detection of Protein Differences by Two-Dimensional Gel Electrophoresis and Computer-Based Differential Displayn Birte Schulenberg and Wayne F. Pattonn n A Strategy for Characterizing Antibody/Antigen Interactions Using ProteinChip® Arraysn Alexandra Huhalov, Daniel I. R. Spencer, and Kerry A. Chestern n Stable Isotope Labeling with Amino Acids as an Aid to Protein Identification in Peptide Mass Fingerprintingn Robert J. Beynonn n The Use of 18O Labeling as a Tool for Proteomic Applicationsn Ian I. Stewart, Ty Thomson, Daniel Figeys, and Henry S. Dueweln n Automated Nanoflow Liquid Chromatography/Tandem Mass Spectrometric Identification of Liver Mitochondrial Proteinsn Bart Devreese, Frank Vanrobaeys, Elke Lecocq, Joél Smet, Rudy Van Coster, and Jozef VanBeeumenn n In Silico Proteomics: Predicting Interactions from Sequencen Joel R. Bock and David A. Goughn n Part II. Post-Translational Modifications, Variants, and Isoformsn n Predicting Glycan Composition from Experimental Mass Using GlycoModn Catherine A. Cooper, Elisabeth Gasteiger, and Nicolle H. Packern n Querying GlycoSuiteDBn Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins, and Nicolle H. Packern n New Tools for Quantitative Phosphoproteome Analysisn Li-Rong Yu, Van M. Hoang, and Timothy D. Veenstran n Computer-Aided Strategies for Characterizing Protein Isoformsn Frédéric Nikitin and Frédérique Lisacekn n Protein Variant Separations Using Cation Exchange Chromatography on Grafted, Polymeric Stationary Phasesn Michael Weitzhandler, Dell Farnan, Nebojsa Avdalovic, and Chris Pohln n Part III. Specific Systemsn n Noninvasive Imaging of Protein-Protein Interactions in Living Animalsn Gary D. Luker, Vijay Sharma, and David Piwnica-Wormsn n Strategies in Clinical Proteomicsn Eric T. Fungn n Proteomic Profiling of the Cancer Microenvironmentn Vladimir Knezevic and Michael R. Emmert-Buckn n Identification of Determinants of Sensitivity to Antitumor Drugsn Paola Perego, Giovanni Luca Beretta, and Laura Gattin n Application of Proteomics to the Discovery of Serological Tumor Markersn Terence C. W. Poon and Philip J. Johnsonn n Infectomic Analysis of Microbial Infections Using Proteomicsn Sheng-He Huang, Ambrose Jong, and James T. Summersgilln n Toward a Complete Proteome of Bacillus subtilis: Cytosolic, Cell Wall-Associated, and Extracellular Proteinsn Haike Antelmann, Jan Maarten van Dijl, and Michael Heckern n Renal and Urinary Proteomicsn Visith Thongboonkerd, Elias Klein, and Jon B. Kleinn n Proteomics in Endocrinologyn Jan W. A. Smit and
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.