Note: Cover -- Advances in Protein Chemistry -- Copyright -- Contents -- Proteomics in the Postgenomic Age -- I. Introduction -- II. Deciphering the Genome -- III. Gene Expression Profiles -- IV. A Niche for Proteomics -- V. The Proteome: Greater than the Sum of its Parts -- VI. Biological and Clinical Applications -- VII. Proteomics Meets Cell Biology -- VIII. Summary -- References -- The Tools of Proteomics -- I. Introduction -- II. Ionization Methods -- III. Mass Analyzers -- IV. Sample Fractionation -- V. Software Tools -- VI. Conclusions -- References -- Proteomic Analysis by Two-Dimensional Polyacrylamide Gel Electrophoresis -- I. Introduction -- II. Historical Development of 2D-PAGE -- III. Limitations and Advances -- IV. Protein Visualization Methods -- V. Proteome Application of 2D-PAGE -- VI. The Future -- Acknowledgments -- References -- High-Performance Separations and Mass Spectrometric Methods for High-Throughput Proteomics Using Accurate Mass Tags -- I. Introduction -- II. Proteome Measurement Technology and Applications -- III. Technology Advances for Expanding Proteome Coverage -- Acknowledgments -- References -- Current Strategies for Quantitative Proteomics -- I. Introduction -- II. Quantitative Two-Dimensional Polyacrylamide Gel Electrophoresis -- III. Metabolic Labeling Applications for Quantitative Proteomics -- IV. Chemical Modification Strategies for Quantitative Proteome Measurements -- V. Conclusions -- Acknowledgments -- References -- Proteome Analysis of Posttranslational Modifications -- I. Introduction -- II. Phosphorylation -- III. Mass Spectral Identification of Phosphopeptides -- IV. Glycosylation -- V. Conclusions -- Acknowledgments -- References -- Mapping Protein Modifications with Liquid Chromatography-Mass Spectrometry and the SALSA Algorithm -- I. Introduction -- II. MS-MS Fragmentation of Modified Peptides. , III. SALSA: A Pattern Recognition Algorithm to Identify MS-MS Spectra for Modified Peptides -- IV. Mapping Protein Modifications with SALSA -- V. Comparison of SALSA with Other Software for Analysis of MS-MS Data -- Acknowledgments -- References -- Emerging Role of Mass Spectrometry in Structural and Functional Proteomics -- I. Introduction -- II. Application of ESI-MS in Structural and Functional Proteomics -- III. Future Directions -- Acknowledgments -- References -- Application of Separation Technologies to Proteomics Research -- I. Introduction -- II. What Is Proteomics? -- III. What Needs to Be Separated? -- IV. Slab Gel Electophoresis, High-Performance Liquid Chromatography, or Capillary Electrophoresis? -- V. Multidimensional Separations of Proteins -- VI. On-Column HPLC and CE Protein Concentration -- VII. Detection -- VIII. Proteome Quantitation Strategies -- IX. Conclusion -- Acknowledgments -- References -- Proteomics of Membrane Proteins -- I. Introduction -- II. Techniques -- III. Applications: The Thylakoid Membrane Proteome -- IV. Conclusions -- Acknowledgments -- References -- Proteomics in Drug Discovery -- I. Introduction -- II. The Complexity of Proteomic Analysis in Drug Discovery -- III. Proteomic Strategies in Drug Discovery -- IV. Quantification in Proteomic Studies -- V. Applications -- VI. Functional Proteomics Approach -- VII. Future Trends in Proteomics -- References -- From Clone to Crystal: Maximizing the Amount of Protein Samples for Structure Determination -- I. Introduction -- II. Technology Drives the Process -- III. From Sequence to Solubility: The First Step -- IV. Alternative Expression Systems -- V. Screening for the Most Soluble Ortholog -- VI. Cofactor Screens -- VII. Solubility Screens -- VIII. From Solubility to Structure: The Second Step -- IX. Conclusions -- References -- Proteomics and Bioinformatics. , I. Introduction -- II. Bioinformatics Tools -- III. Proteomics Tools -- IV. Database Integration -- V. Conclusions -- Acknowledgments -- References -- AUTHOR INDEX -- SUBJECT INDEX.