Handbook of Proteomic Methods

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 Array 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 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 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, Joél Smet, Rudy Van Coster, and Jozef VanBeeumen In Silico 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 Frédéric Nikitin and Frédérique 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 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