Handbook of Proteomic Methods
Samenvatting
The developing new field of proteomics holds significant promise for a deeper understanding of complicated biological systems, as well as for novel approaches to the cure of disease. In the Handbook of Proteomic Methods, P. Michael Conn has assembled a panel of well-recognized experts to describe a wide range of powerful techniques for identifying and analyzing the diversity of proteins expressed in cells.
These readily reproducible proteomic methods range from general to specific techniques, and include methods for data analysis, post-translational 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. Each fully tested protocol is described in step-by-step detail, complete with tricks of the trade and hints on avoiding pitfalls. The detail of description exceeds that usually found in primary publications.
Wide-ranging and practical, the Handbook of Proteomic Methods offers scientists entering, or already active in, the field a fully referenced compendium of easy-to-use proteomic methods-each reflecting the power and promise of proteomics in illuminating complex biological systems and in promoting the development of novel drugs for the amelioration of disease.
Specificaties
Inhoudsopgave
Contributors
PART I: GENERAL TECHNIQUES
1. Proteomics and the Molecular Biologist
Paul R. Graves and Timothy A. J. Haystead
2. 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
3. Selective Chemical Cleavage Methods in Proteomics, Including C-Terminal Successive Degradation
Akira Tsugita
4. Means of Hydrolyzing Proteins Isolated upon ProteinChip Array Surfaces: Chemical and Enzymatic Approaches
Shanhua Lin, Ning Tang, and Scot R. Weinberger
5. 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
6. Qualitative and Quantitative Proteomic Analyses via Multidimensional Protein Identification Technology
Michael P. Washburn and David M. Schieltz
7. Di- and Tri-Chromatic Fluorescence Detection on Western Blots
Karen J. Martin and Wayne F. Patton
8. Multiplexed Proteomics: Fluorescence Detection of Protein Differences by Two-Dimensional Gel Electrophoresis and Computer-Based Differential Display
Birte Schulenberg and Wayne F. Patton
9. A Strategy for Characterizing Antibody/Antigen Interactions Using ProteinChip® Arrays
Alexandra Huhalov, Daniel I. R. Spencer, and Kerry A. Chester
10. Stable Isotope Labeling with Amino Acids as an Aid to Protein Identification in Peptide
Mass Fingerprinting
Robert J. Beynon
11. The Use of 18O Labeling as a Tool for Proteomic Applications
Ian I. Stewart, Ty Thomson, Daniel Figeys, and Henry S. Duewel
12. 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 Van Beeumen
13. In Silico Proteomics: Predicting Interactions from Sequence
Joel R. Bock and David A. Gough
PART II: POST-TRANSLATIONAL MODIFICATIONS, VARIANTS, AND ISOFORMS
14. Predicting Glycan Composition from Experimental Mass Using GlycoMod
Catherine A. Cooper, Elisabeth Gasteiger, and Nicolle H. Packer
15. Querying GlycoSuiteDB
Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins, and Nicolle H. Packer
16. New Tools for Quantitative Phosphoproteome Analysis
Li-Rong Yu, Van M. Hoang, and Timothy D. Veenstra
17 Computer-Aided Strategies for Characterizing Protein Isoforms
Frédéric Nikitin and Frédérique Lisacek
18. 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
19. Noninvasive Imaging of Protein–Protein Interactions in Living Animals
Gary D. Luker, Vijay Sharma, and David Piwnica-Worms
20. Strategies in Clinical Proteomics
Eric T. Fung
21. Proteomic Profiling of the Cancer Microenvironment
Vladimir Knezevic and Michael R. Emmert-Buck
22. Identification of Determinants of Sensitivity to Antitumor Drugs
Paola Perego, Giovanni Luca Beretta, and Laura Gatti
23. Application of Proteomics to the Discovery of Serological Tumor Markers
Terence C. W. Poon and Philip J. Johnson
24. Infectomic Analysis of Microbial Infections Using Proteomics
Sheng-He Huang, Ambrose Jong, and James T. Summersgill
25. Toward a Complete Proteome of Bacillus subtilis: Cytosolic, Cell Wall-Associated, and Extracellular Proteins
Haike Antelmann, Jan Maarten van Dijl, and Michael Hecker
26. Renal and Urinary Proteomics
Visith Thongboonkerd, Elias Klein, and Jon B. Klein
27. Proteomics in Endocrinology
Jan W. A. Smit and Johannes A. Romijn
28. Proteomics in Plant Biology
Christina Mihr and Hans-Peter Braun
PART IV: DATA ANALYSIS
29. Bioinformatics in Proteomics
Mauno Vihinen
30. Quantitative Characterization of Proteomics Maps by Matrix Invariants
Milan Randi´c
31. Complexity of Protein–Protein Interaction Networks, Complexes, and Pathways
Danail Bonchev
32. Patchwork Peptide Sequencing: Protein Identification by Accurate Mass-to-Sequence Conversion of High-Resolution Q-TOF Tandem Mass Spectrometry Data
Andreas Schlosser and Wolf D. Lehmann
33. Estimation of Bias in Proteome Research
Ralf Mrowka and Hanspeter Herzel
34. Scoring Functions for Mass Spectrometric Protein Identification
Robin Gras, Patricia Hernandez, Markus Müller, and Ron D. Appel
Index
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