Proteins and Proteomics

  1. Applications and Frontiers of Proteomics
    1. Clinical Proteomics and Biomarker Discovery
      1. Disease Diagnosis and Prognosis
        1. Cancer Biomarkers
          1. Cardiovascular Disease Markers
            1. Neurological Disorder Indicators
              1. Infectious Disease Diagnostics
              2. Monitoring Treatment Response
                1. Drug Efficacy Assessment
                  1. Resistance Mechanisms
                    1. Adverse Effect Prediction
                    2. Personalized Medicine
                      1. Patient Stratification
                        1. Precision Therapeutics
                          1. Pharmacoproteomics
                          2. Clinical Validation Pipeline
                            1. Discovery Phase
                              1. Verification Phase
                                1. Validation Phase
                                  1. Implementation Challenges
                                2. Drug Discovery and Development
                                  1. Target Identification and Validation
                                    1. Disease-Associated Proteins
                                      1. Druggability Assessment
                                        1. Target Prioritization
                                        2. Off-target Effect Analysis
                                          1. Polypharmacology
                                            1. Safety Assessment
                                              1. Selectivity Profiling
                                              2. Drug Mechanism of Action Studies
                                                1. Target Engagement
                                                  1. Pathway Modulation
                                                    1. Resistance Mechanisms
                                                    2. Pharmacokinetics and Pharmacodynamics
                                                      1. ADMET Properties
                                                        1. Biomarker Development
                                                      2. Systems Biology
                                                        1. Integration with Genomics
                                                          1. Genotype-Phenotype Relationships
                                                            1. Genetic Variation Effects
                                                              1. Epistatic Interactions
                                                              2. Integration with Transcriptomics
                                                                1. mRNA-Protein Correlations
                                                                  1. Post-Transcriptional Regulation
                                                                    1. Temporal Dynamics
                                                                    2. Integration with Metabolomics
                                                                      1. Enzyme-Metabolite Networks
                                                                        1. Flux Analysis
                                                                          1. Metabolic Phenotyping
                                                                          2. Multi-omics Data Analysis
                                                                            1. Data Integration Strategies
                                                                              1. Network-Based Approaches
                                                                                1. Machine Learning Applications
                                                                                2. Mathematical Modeling
                                                                                  1. Kinetic Models
                                                                                    1. Boolean Networks
                                                                                      1. Constraint-Based Models
                                                                                    2. Understanding Disease Pathophysiology
                                                                                      1. Cancer Proteomics
                                                                                        1. Tumor Biomarker Discovery
                                                                                          1. Diagnostic Markers
                                                                                            1. Prognostic Indicators
                                                                                              1. Predictive Biomarkers
                                                                                              2. Tumor Microenvironment Analysis
                                                                                                1. Stromal Interactions
                                                                                                  1. Immune Cell Profiling
                                                                                                    1. Angiogenesis Factors
                                                                                                    2. Metastasis Mechanisms
                                                                                                      1. Invasion Pathways
                                                                                                        1. Circulating Tumor Cells
                                                                                                        2. Drug Resistance Studies
                                                                                                          1. Resistance Mechanisms
                                                                                                            1. Combination Therapies
                                                                                                          2. Neuroproteomics
                                                                                                            1. Neurodegenerative Disease Studies
                                                                                                              1. Alzheimer's Disease
                                                                                                                1. Parkinson's Disease
                                                                                                                  1. ALS and Other Motor Neuron Diseases
                                                                                                                  2. Synaptic Proteome Analysis
                                                                                                                    1. Synaptic Plasticity
                                                                                                                      1. Neurotransmitter Systems
                                                                                                                      2. Brain Region-Specific Proteomes
                                                                                                                        1. Cortical vs Subcortical
                                                                                                                          1. Developmental Changes
                                                                                                                        2. Cardiovascular Proteomics
                                                                                                                          1. Heart Disease Biomarkers
                                                                                                                            1. Myocardial Infarction
                                                                                                                              1. Heart Failure
                                                                                                                                1. Arrhythmias
                                                                                                                                2. Vascular Proteome Profiling
                                                                                                                                  1. Atherosclerosis
                                                                                                                                    1. Endothelial Function
                                                                                                                                      1. Hypertension
                                                                                                                                    2. Immunoproteomics
                                                                                                                                      1. Autoimmune Diseases
                                                                                                                                        1. Vaccine Development
                                                                                                                                          1. Transplant Rejection
                                                                                                                                        2. Chemical Proteomics
                                                                                                                                          1. Probing Protein-Small Molecule Interactions
                                                                                                                                            1. Target Identification
                                                                                                                                              1. Binding Site Mapping
                                                                                                                                                1. Selectivity Profiling
                                                                                                                                                2. Activity-Based Protein Profiling
                                                                                                                                                  1. Enzyme Activity Measurement
                                                                                                                                                    1. Inhibitor Screening
                                                                                                                                                      1. Functional Annotation
                                                                                                                                                      2. Target Deconvolution
                                                                                                                                                        1. Phenotypic Screening Follow-up
                                                                                                                                                          1. Mechanism of Action Studies
                                                                                                                                                          2. Chemical Genetics
                                                                                                                                                            1. Small Molecule Perturbations
                                                                                                                                                              1. Pathway Dissection
                                                                                                                                                            2. Emerging Technologies and Future Directions
                                                                                                                                                              1. Single-Cell Proteomics
                                                                                                                                                                1. Technical Challenges
                                                                                                                                                                  1. Method Development
                                                                                                                                                                    1. Cellular Heterogeneity
                                                                                                                                                                      1. Disease Applications
                                                                                                                                                                      2. Spatial Proteomics
                                                                                                                                                                        1. Tissue Imaging
                                                                                                                                                                          1. Subcellular Localization
                                                                                                                                                                            1. Proximity Proteomics
                                                                                                                                                                              1. Multiplexed Imaging
                                                                                                                                                                              2. Artificial Intelligence in Proteomics
                                                                                                                                                                                1. Machine Learning Applications
                                                                                                                                                                                  1. Spectrum Identification
                                                                                                                                                                                    1. Retention Time Prediction
                                                                                                                                                                                      1. Protein Structure Prediction
                                                                                                                                                                                      2. Deep Learning Approaches
                                                                                                                                                                                        1. Neural Networks
                                                                                                                                                                                          1. Feature Learning
                                                                                                                                                                                          2. Data Mining and Pattern Recognition
                                                                                                                                                                                          3. High-Throughput and Automation Advances
                                                                                                                                                                                            1. Robotic Sample Preparation
                                                                                                                                                                                              1. Miniaturization Technologies
                                                                                                                                                                                                1. Multiplexed Assays
                                                                                                                                                                                                  1. Real-Time Analysis
                                                                                                                                                                                                  2. Structural Proteomics Integration
                                                                                                                                                                                                    1. Cryo-EM and Proteomics
                                                                                                                                                                                                      1. Cross-Linking MS
                                                                                                                                                                                                        1. Hydrogen-Deuterium Exchange
                                                                                                                                                                                                        2. Proteogenomics
                                                                                                                                                                                                          1. Genome Annotation
                                                                                                                                                                                                            1. Variant Peptide Detection
                                                                                                                                                                                                              1. Alternative Splicing Analysis

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                                                                                                                                                                                                          11. Proteomic Data Analysis and Bioinformatics

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                                                                                                                                                                                                          1. Fundamentals of Proteins