Proteins and Proteomics

  1. Proteomic Data Analysis and Bioinformatics
    1. Mass Spectra Processing
      1. Raw Data Formats
        1. Vendor-Specific Formats
          1. Open Standards
          2. Feature Detection and Deconvolution
            1. Peak Picking Algorithms
              1. Isotope Pattern Recognition
                1. Charge State Determination
                2. Spectrum Quality Assessment
                  1. Signal-to-Noise Ratios
                    1. Spectral Quality Metrics
                    2. Noise Reduction and Baseline Correction
                      1. Smoothing Algorithms
                        1. Background Subtraction
                        2. Retention Time Alignment
                          1. Chromatographic Drift Correction
                            1. Landmark-Based Alignment
                          2. Protein Identification from MS/MS Data
                            1. Database Search Engines
                              1. Mascot
                                1. Probability-Based Scoring
                                  1. Ion Score Calculation
                                  2. Sequest
                                    1. Cross-Correlation Scoring
                                      1. Preliminary Scoring
                                      2. MaxQuant
                                        1. Andromeda Search Engine
                                          1. Label-Free Quantification
                                          2. X!Tandem
                                            1. Open Source Platform
                                            2. MS-GF+
                                              1. Generating Function Approach
                                            3. Search Parameters
                                              1. Database Selection
                                                1. Enzyme Specificity
                                                  1. Modification Settings
                                                    1. Mass Tolerances
                                                    2. De Novo Sequencing
                                                      1. Spectrum Interpretation
                                                        1. Sequence Tags
                                                          1. Hybrid Approaches
                                                          2. Statistical Validation and False Discovery Rate (FDR)
                                                            1. Target-Decoy Strategy
                                                              1. q-Value Calculation
                                                                1. Percolator and PeptideProphet
                                                                2. Peptide-Spectrum Matching
                                                                  1. Scoring Functions
                                                                    1. Confidence Assessment
                                                                    2. Protein Inference
                                                                      1. Shared Peptides Problem
                                                                        1. Protein Groups
                                                                          1. Parsimony Principle
                                                                        2. Protein Quantification
                                                                          1. Label-Free Quantification (LFQ)
                                                                            1. Spectral Counting
                                                                              1. Normalization Methods
                                                                                1. Statistical Testing
                                                                                2. Intensity-Based Methods
                                                                                  1. Peak Integration
                                                                                    1. Missing Value Imputation
                                                                                  2. Isotope Labeling Methods
                                                                                    1. SILAC Data Analysis
                                                                                      1. Ratio Calculation
                                                                                        1. Outlier Detection
                                                                                        2. iTRAQ and TMT Analysis
                                                                                          1. Reporter Ion Quantification
                                                                                            1. Interference Correction
                                                                                            2. Experimental Design Considerations
                                                                                              1. Randomization
                                                                                                1. Blocking Factors
                                                                                              2. Statistical Analysis
                                                                                                1. Differential Expression Testing
                                                                                                  1. Multiple Testing Correction
                                                                                                    1. Effect Size Estimation
                                                                                                      1. Power Analysis
                                                                                                    2. Bioinformatic Interpretation
                                                                                                      1. Functional Annotation
                                                                                                        1. Gene Ontology (GO)
                                                                                                          1. Biological Process
                                                                                                            1. Molecular Function
                                                                                                              1. Cellular Component
                                                                                                              2. Protein Family Classification
                                                                                                                1. Pfam Domains
                                                                                                                  1. InterPro Database
                                                                                                                    1. SMART Domains
                                                                                                                    2. Enzyme Classification
                                                                                                                      1. EC Numbers
                                                                                                                        1. KEGG Orthology
                                                                                                                      2. Pathway Analysis
                                                                                                                        1. KEGG Pathways
                                                                                                                          1. Metabolic Pathways
                                                                                                                            1. Signaling Pathways
                                                                                                                            2. Reactome
                                                                                                                              1. Pathway Hierarchy
                                                                                                                                1. Pathway Enrichment
                                                                                                                                2. Gene Set Enrichment Analysis
                                                                                                                                  1. Enrichment Statistics
                                                                                                                                    1. Leading Edge Analysis
                                                                                                                                  2. Protein-Protein Interaction Network Analysis
                                                                                                                                    1. Network Construction
                                                                                                                                      1. Interaction Databases
                                                                                                                                        1. Confidence Scoring
                                                                                                                                        2. Network Properties
                                                                                                                                          1. Centrality Measures
                                                                                                                                            1. Clustering Coefficients
                                                                                                                                              1. Network Motifs
                                                                                                                                              2. Module Detection
                                                                                                                                                1. Community Detection Algorithms
                                                                                                                                                  1. Functional Modules
                                                                                                                                                2. Data Visualization
                                                                                                                                                  1. Volcano Plots
                                                                                                                                                    1. Fold Change vs Significance
                                                                                                                                                      1. Multiple Testing Visualization
                                                                                                                                                      2. Heatmaps
                                                                                                                                                        1. Hierarchical Clustering
                                                                                                                                                          1. Expression Patterns
                                                                                                                                                          2. Network Maps
                                                                                                                                                            1. Node and Edge Attributes
                                                                                                                                                              1. Layout Algorithms
                                                                                                                                                              2. Principal Component Analysis (PCA)
                                                                                                                                                                1. Dimensionality Reduction
                                                                                                                                                                  1. Sample Clustering
                                                                                                                                                                  2. MA Plots
                                                                                                                                                                    1. Box Plots and Violin Plots
                                                                                                                                                                  3. Data Repositories and Standards
                                                                                                                                                                    1. ProteomeXchange
                                                                                                                                                                      1. Data Submission Standards
                                                                                                                                                                        1. Partner Repositories
                                                                                                                                                                        2. PRIDE Database
                                                                                                                                                                          1. Data Storage and Access
                                                                                                                                                                            1. Metadata Standards
                                                                                                                                                                            2. Data Sharing and FAIR Principles
                                                                                                                                                                              1. Findable, Accessible, Interoperable, Reusable
                                                                                                                                                                                1. Metadata Standards
                                                                                                                                                                                  1. Data Formats
                                                                                                                                                                                  2. Quality Control Standards
                                                                                                                                                                                    1. Minimum Information Guidelines
                                                                                                                                                                                      1. Experimental Validation

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                                                                                                                                                                                  10. Analysis of Protein Interactions

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                                                                                                                                                                                  12. Applications and Frontiers of Proteomics