Perspectives for mass spectrometry and functional proteomics

I. Introduction 2 II. Why Functional Proteomics? 3 A. The Complementarity of Genomics and Proteomics 3 B. Genotypes and Protein Phenotypes 3 C. New Views of Biological Function 5 D. The Role of Mass Spectrometry 6 E. Current General Areas of Proteome Research 7 1. Mapping of Total Cellular Proteins 7 2. Subcellular Complexes and Organelles 10 3. Protein Phenotypes and Function 13 F. The Need for and Utility of Functional Proteomics 15 1. Definition of Functional Proteomics. 15 2. A New Biology—Networks, Fluxes, and Dynamics at the Molecular Level 16 3. The Importance of Assigning Gene Functions in Context 16 4. Practical Advantages of Functional Proteomics 17 III. Recent Applications of Functional Proteomics and Mass Spectrometry 17 A. Changes in Cellular Environment 17 B. Direct Observation of Growth Factor Signal Transduction 19 C. Protein Synthesis Following Directed Cellular Perturbation 22 D. Directed Measurement of Functional Classes of Proteins 24 E. Global Detection of Specific Types of Functional Activities in Cells 25 F. Investigating the Function of Individual Proteins 26 G. Summary 29 IV. Technical Advances for Functional Proteomics 29 A. "Total" Proteins 29 B. Display Methodologies 31 C. Quantification Methods 33 1. Chemical Staining 33 2. Antibody-Based Detection Methods 33 3. New Multi-Photon Detection Methods for Detection of Radioactive Labels 34 D. Implications for Automation 34 V. Perspectives 36 A. Directions for Functional Proteomics 36 1. Studies of Cells in Culture 36 2. Single Cells 36 3. Tissue Samples 37 4. Medical and Pharmaceutical Themes 37 5. Comparative Proteomics 37 B. Perturbation Methods—The Importance of Time Scales, Kinetics, and Fluxes 38 C. The "Virtual Proteome" 39 D. Constructing the "Virtual Proteome": Community-Based Proteomics 42 1. Standards for Display Maps of the Proteome 43 2. Standards for Mass Spectrometric Identification of Proteins 43 3. Databases 44 E. Implications for Mass Spectrometry 45 1. Sensitivity and Functional Proteomics 45 2. Phenotypic Characterization of Proteins 46 3. Automated Analysis of MS Data in Proteomics 47 F. Conclusion 48 Acknowledgments 48 References 48