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Table of Contents:

 

Part I. General Techniques

 

1. Proteomics and the Molecular Biologist 3

2. Protein Identification from 2-D Gels Using In Vitro Transcription Translation Products 17

3. Selective Chemical Cleavage Methods in Proteomics, Including C-Terminal Successive Degradation 29

4. Means of Hydrolyzing Proteins Isolated upon ProteinChip Array Surfaces 59

5. A Combined Radiolabeling and Silver Staining Technique for Improved Visualization and Localization of Proteins on Two-Dimensional Gels 73

6. Qualitative and Quantitative Proteomic Analyses via Multidimensional Protein Identification Technology 79

7. Di- and Tri-Chromatic Fluorescence Detection on Western Blots 93

8. Multiplexed Proteomics 107

9. A Strategy for Characterizing Antibody/Antigen Interactions Using ProteinChip Arrays 117

10. Stable Isotope Labeling with Amino Acids as an Aid to Protein Identification in Peptide Mass Fingerprinting 129

11. The Use of 18O Labeling as a Tool for Proteomic Applications 145

12. Automated Nanoflow Liquid Chromatography/Tandem Mass Spectrometric Identification of Liver Mitochondrial Proteins 181

13. In Silico Proteomics 193

 

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

 

1. Predicting Glycan Composition from Experimental Mass Using GlycoMod 225

2. Querying GlycoSuiteDB 233

3. New Tools for Quantitative Phosphoproteome Analysis 241

4. Computer-Aided Strategies for Characterizing Protein Isoforms 259

5. Protein Variant Separations Using Cation Exchange Chromatography on Grafted, Polymeric Stationary Phases 269

 

Part III. Specific Systems

 

1. Noninvasive Imaging of Protein-Protein Interactions in Living Animals 283

2. Strategies in Clinical Proteomics 299

3. Proteomic Profiling of the Cancer Microenvironment 309

4. Identification of Determinants of Sensitivity to Antitumor Drugs 319

5. Ap0plication of Proteomics to the Discovery of Serological Tumor Markers 331

6. Infectiomic Analysis of Microbial Infections Using Proteomics 347

7. Toward a Complete Proteome of Bacillus subtilis 357

8. Renal and Urinary Proteomics 375

9. Proteomics in Endocrinology 397

10. Proteomics in Plant biology 409

 

Part IV. Data Analysis

 

1. Bioinformatics in Proteomics 419

2. Quantitative Characterization of Proteomics Maps by Matrix Invariants 429

3. Complexity of Protein-Protein Interaction Networks, Complexes, and Pathways 451

4. Patchwork Peptide Sequencing 463

5. Estimation of Bias in Proteome Research 473

6. Scoring Functions for Mass Spectrometric Protein Identification 477

 

Index 487

 

Handbook of Proteomic Methods includes wide range of techniques for identifying and analyzing proteins expressed in cells. This monograph is valuable for beginners and experienced researchers alike with its detailed descriptions of proteomic methods from data analysis to posttranslational modification. The methods vary from more general methods useful in antitumor drug research to more specific fields like endocrinology and plant biology. As many other Humana Press methods books, this is another must-have for large academic libraries supporting research in complex biological systems and drug development.