Bioinformatics

1. Proteomics
   1. Overview of Proteomics
      1. Definition and scope
      2. Historical development of proteomics
      3. Relation to genomics and transcriptomics
      4. Importance and applications
   2. Protein Structure
      1. Levels of protein structure
         1. Primary, secondary, tertiary, and quaternary structures
      2. Techniques for studying protein structure
         1. X-ray crystallography
         2. NMR spectroscopy
         3. Cryo-electron microscopy
   3. Protein Identification and Function Prediction
      1. Proteome analysis strategies
         1. Bottom-up proteomics
         2. Top-down proteomics
      2. Protein annotation methods
         1. Homology-based function prediction
         2. Functional domain identification
      3. Bioinformatic tools for protein annotation
         1. Pfam
         2. InterPro
   4. Mass Spectrometry in Proteomics
      1. Fundamentals of mass spectrometry
      2. Types of mass spectrometers used
         1. Time-of-flight (TOF)
         2. Orbitrap
         3. Tandem mass spectrometry (MS/MS)
      3. Sample preparation techniques
         1. In-gel digestion
         2. In-solution digestion
      4. Data analysis in mass spectrometry
         1. Peak identification
         2. Quantitative proteomics
         3. Label-free vs. labeled methods (iTRAQ, SILAC, etc.)
   5. Protein Interaction Networks
      1. Types of protein-protein interactions
      2. Experimental methods for detecting interactions
         1. Yeast two-hybrid screening
         2. Co-immunoprecipitation
         3. Cross-linking mass spectrometry
      3. Computational methods for predicting interactions
      4. Visualization tools for interaction networks
         1. Cytoscape
   6. Post-Translational Modifications (PTMs)
      1. Types of PTMs
         1. Phosphorylation
         2. Glycosylation
         3. Ubiquitination
      2. Methods for detecting PTMs
         1. Enrichment techniques
         2. Mass spectrometry-based approaches
      3. Bioinformatics resources for PTM analysis
         1. PhosphoSitePlus
         2. UniProtKB for PTM annotations
   7. Quantitative Proteomics
      1. Techniques for quantitation
         1. Isotope-coded affinity tags (ICAT)
         2. Tandem mass tags (TMT)
      2. Applications in biomarker discovery
      3. Challenges in analytical reproducibility
   8. Challenges and Future Directions in Proteomics
      1. High-throughput data management
      2. Integration with other omics data
      3. Personalized proteomics
      4. Emerging technologies and trends
         1. Single-cell proteomics
         2. Novel mass spectrometry techniques