Proteins and Proteomics

  1. Quantitative Proteomics
    1. Label-Free Quantification (LFQ)
      1. Spectral Counting
        1. Protein Abundance Index
          1. Normalized Spectral Abundance Factor
            1. Distributed Normalized Spectral Abundance Factor
            2. Intensity-Based Methods
              1. Peak Area Integration
                1. Extracted Ion Chromatograms
                  1. Retention Time Alignment
                  2. Advantages and Limitations
                    1. Sample Throughput
                      1. Dynamic Range
                        1. Reproducibility Challenges
                      2. Isotope Labeling Methods
                        1. Metabolic Labeling
                          1. SILAC (Stable Isotope Labeling by Amino Acids in Cell Culture)
                            1. Heavy Amino Acids
                              1. Incorporation Efficiency
                                1. Multiplexing Capabilities
                                2. 15N Labeling
                                  1. Whole Organism Labeling
                                    1. Plant and Microbial Systems
                                  2. Chemical Labeling
                                    1. iTRAQ (Isobaric Tags for Relative and Absolute Quantitation)
                                      1. Reagent Chemistry
                                        1. Multiplexing Levels
                                          1. Quantification Accuracy
                                          2. TMT (Tandem Mass Tags)
                                            1. TMT Chemistry
                                              1. Interference Issues
                                              2. ICAT (Isotope-Coded Affinity Tags)
                                                1. Cysteine-Specific Labeling
                                                  1. Affinity Purification
                                                2. Enzymatic Labeling
                                                  1. 18O Labeling
                                                    1. Protease-Catalyzed Exchange
                                                      1. Quantification Principles
                                                    2. Experimental Design Considerations
                                                      1. Biological vs Technical Replicates
                                                        1. Sample Pooling Strategies
                                                          1. Statistical Power Analysis
                                                        2. Absolute Quantification
                                                          1. Protein Standard Absolute Quantification (PSAQ)
                                                            1. Quantification Concatemer (QconCAT)
                                                              1. Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA)
                                                                1. Parallel Reaction Monitoring for Absolute Quantification

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                                                              8. Core Technologies in Proteomics

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                                                              10. Analysis of Protein Interactions