Proteins and Proteomics

  1. Introduction to Proteomics
    1. Defining the Proteome
      1. Contrast with Genome and Transcriptome
        1. Genetic Information Flow
          1. Complexity Differences
          2. Dynamic Nature of the Proteome
            1. Temporal Changes
              1. Cell Cycle Variations
                1. Circadian Rhythms
                  1. Aging Effects
                  2. Spatial Differences
                    1. Tissue-Specific Expression
                      1. Subcellular Localization
                        1. Organellar Proteomes
                        2. Environmental and Developmental Influences
                          1. Stress Responses
                            1. Differentiation Programs
                              1. Disease States
                            2. Proteome Complexity
                              1. Alternative Splicing
                                1. Post-Translational Modifications
                                  1. Protein Isoforms
                                    1. Dynamic Range of Expression
                                  2. Goals and Scope of Proteomics
                                    1. Protein Identification and Profiling
                                      1. Comprehensive Protein Catalogs
                                        1. Expression Profiling
                                        2. Quantification of Protein Expression
                                          1. Absolute vs Relative Quantification
                                            1. Comparative Proteomics
                                            2. Characterization of PTMs
                                              1. Modification Site Mapping
                                                1. Stoichiometry Determination
                                                2. Mapping Protein-Protein Interactions
                                                  1. Interaction Networks
                                                    1. Complex Composition
                                                    2. Determining Subcellular Localization
                                                      1. Organellar Proteomics
                                                        1. Spatial Organization
                                                        2. Functional Annotation
                                                          1. Protein Function Prediction
                                                            1. Pathway Analysis
                                                          2. Major Branches of Proteomics
                                                            1. Expression Proteomics
                                                              1. Comparative Expression Analysis
                                                                1. Biomarker Discovery
                                                                  1. Disease Proteomics
                                                                  2. Structural Proteomics
                                                                    1. High-Throughput Structure Determination
                                                                      1. Structural Genomics Initiatives
                                                                      2. Functional Proteomics
                                                                        1. Protein Function Elucidation
                                                                          1. Interaction Mapping
                                                                            1. Activity Profiling
                                                                            2. Clinical Proteomics
                                                                              1. Diagnostic Applications
                                                                                1. Therapeutic Target Discovery
                                                                                2. Comparative Proteomics
                                                                                  1. Species Comparisons
                                                                                    1. Evolutionary Proteomics
                                                                                  2. Historical Development
                                                                                    1. Early Protein Separation Methods
                                                                                      1. Mass Spectrometry Revolution
                                                                                        1. Genomics Integration
                                                                                          1. Current Technological Advances

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                                                                                        6. Regulation of Protein Activity

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                                                                                        8. Core Technologies in Proteomics