Handbook of Proteomic Methods

by Conn, P. Michael

• ISBN13: 9781588293404
• ISBN10: 1588293408
• Format: Hardcover
• Copyright: 2003-08-01
• Publisher: Humana Pr Inc

Summary

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.

Table of Contents

Preface	v
Contributors	xi
Part I. General Techniques
Proteomics and the Molecular Biologist	3	(14)
Paul R. Graves
Timothy A. J. Haystead
Protein Identification from 2-D Gels Using In Vitro Transcription Translation Products	17	(12)
Nathalie Norais
Renzo Nogarotto
Emilia Tiziana lacobini
Ignazio Garaguso
Renata Grifantini
Giuliano Galli
Guido Grandi
Selective Chemical Cleavage Methods in Proteomics, Including C-Terminal Successive Degradation	29	(30)
Akira Tsugita
Means of Hydrolyzing Proteins Isolated upon ProteinChip Array Surfaces: Chemical and Enzymatic Approaches	59	(14)
Shanhua Lin
Ning Tang
Scot R. Weinberger
A Combined Radiolabeling and Silver Staining Technique for Improved Visualization and Localization of Proteins on Two-Dimensional Gels	73	(6)
Jules A. Westbrook
Michael J. Dunn
Qualitative and Quantitative Proteomic Analyses via Multidimensional Protein Identification Technology	79	(14)
Michael P. Washburn
David M. Schieltz
Di- and Tri-Chromatic Fluorescence Detection on Western Blots	93	(14)
Karen J. Martin
Wayne F. Patton
Multiplexed Proteomics: Fluorescence Detection of Protein Differences by Two-Dimensional Gel Electrophoresis and Computer-Based Differential Display	107	(10)
Birte Schulenberg
Wayne F. Patton
A Strategy for Characterizing Antibody/Antigen Interactions Using ProteinChip® Arrays	117	(12)
Alexandra Huhalov
Daniel I. R. Spencer
Kerry A. Chester
Stable Isotope Labeling with Amino Acids as an Aid to Protein Identification in Peptide Mass Fingerprinting	129	(16)
Robert J. Beynon
The Use of 18O Labeling as a Tool for Proteomic Applications	145	(36)
Ian I. Stewart
Ty Thomson
Daniel Figeys
Henry S. Duewel
Automated Nanoflow Liquid Chromatography/Tandem Mass Spectrometric Identification of Liver Mitochondrial Proteins	181	(12)
Bart Devreese
Frank Vanrobaeys
Elke Lecocq
Joel Smet
Rudy Van Coster
Jozef Van Beeumen
In Silico Proteomics: Predicting Interactions from Sequence	193	(32)
Joel R. Bock
David A. Gough
Part II. Post-Translational Modifications, Variants, and Isoforms
Predicting Glycan Composition from Experimental Mass Using GlycoMod	225	(8)
Catherine A. Cooper
Elisabeth Gasteiger
Nicolle H. Packer
Querying GlycoSuiteDB	233	(8)
Catherine A. Cooper
Hiren J. Joshi
Mathew J. Harrison
Marc R. Wilkins
Nicolle H. Packer
New Tools for Quantitative Phosphoproteome Analysis	241	(18)
Li-Rong Yu
Van M. Hoang
Timothy D. Veenstra
Computer-Aided Strategies for Characterizing Protein Isoforms	259	(10)
Frederic Nikitin
Frederique Lisacek
Protein Variant Separations Using Cation Exchange Chromatography on Grafted, Polymeric Stationary Phases	269	(14)
Michael Weitzhandler
Dell Farnan
Nebojsa Avdalovic
Chris Pohl
Part III. Specific Systems
Noninvasive Imaging of Protein-Protein Interactions in Living Animals	283	(16)
Gary D. Luker
Vijay Sharma
David Piwnica-Worms
Strategies in Clinical Proteomics	299	(10)
Eric T. Fung
Proteomic Profiling of the Cancer Microenvironment	309	(10)
Vladimir Knezevic
Michael R. Emmert-Buck
Identification of Determinants of Sensitivity to Antitumor Drugs	319	(12)
Paola Perego
Giovanni Luca Beretta
Laura Gatti
Application of Proteomics to the Discovery of Serological Tumor Markers	331	(16)
Terence C. W. Poon
Philip J. Johnson
Infectomic Analysis of Microbial Infections Using Proteomics	347	(10)
Sheng-He Huang
Ambrose Jong
James T. Summersgill
Toward a Complete Proteome of Bacillus subtilis: Cytosolic, Cell Wall-Associated, and Extracellular Proteins	357	(18)
Haike Antelmann
Jan Maarten van Dijl
Michael Hecker
Renal and Urinary Proteomics	375	(22)
Visith Thongboonkerd
Elias Klein
Jon B. Klein
Proteomics in Endocrinology	397	(12)
Jan W. A. Smit
Johannes A. Romijn
Proteomics in Plant Biology	409	(10)
Christina Mihr
Hans-Peter Braun
Part IV. Data Analysis
Bioinformatics in Proteomics	419	(10)
Mauno Vihinen
Quantitative Characterization of Proteomics Maps by Matrix Invariants	429	(22)
Milan Randic
Complexity of Protein-Protein Interaction Networks, Complexes, and Pathways	451	(12)
Danail Bonchev
Patchwork Peptide Sequencing: Protein Identification by Accurate Mass-to-Sequence Conversion of High-Resolution Q-TOF Tandem Mass Spectrometry Data	463	(10)
Andreas Schlosser
Wolf D. Lehmann
Estimation of Bias in Proteome Research	473	(4)
Ralf Mrowka
Hanspeter Herzel
Scoring Functions for Mass Spectrometric Protein Identification	477	(10)
Robin Gras
Patricia Hernandez
Markus Muller
Ron D. Appel
Index	487