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    Proteomics Proteomics Presentation Transcript

    • Proteomics For any given species, the space of possible biomolecules and their organization into pathways and processes is large but finite. BY SRITANU DAS MAHAPATRA ASIA-PACIFIC INSTITUTE OF MANAGEMENT STUDIES
      • In theory, therefore, the biological systems operating in a species can be described comprehensively if a sufficient density of observations on all the elements that constitute the system can be obtained.
    • Proteomics
      • Initial goal was to rapidly identify all the proteins expressed by a cell or tissue – a goal that has yet to be achieved for any species!
      • There are more molecular genetic ways to study proteins and more biochemical ways
    • How to organize information?
      • Gene Ontology
        • Biological process
          • Frequently from biochemical analyses
          • In silico analysis
        • Molecular function
          • Biochemical analysis
        • Cellular component
          • Biochemical analysis
          • GFP or other tagging
        • Interactions
          • MS
          • Two-hybrid
          • Other methods
    • Transposon tagging to identify ORFS Why include a URA3 gene? Why have a lacZ lacking a promoter? Why would you want to cut out all the intervening DNA?
    • High throughput tests of function
    • Yeast deletion strains
    • Microscopic localization
    • microscopy
    • Process for protein isolation
    • 2D gel electrophoresis
    • Antibody arrays Good for low-abundance proteins Problem is antibody specificity
    • Array-based protein interaction detection
    • Protein microarrays
    • Caveats
      • The technology of proteomics is not as mature as genomics, owing to the lack of amplification schemes akin to PCR. Only proteins from a natural source can be analyzed
      • The complexities of the proteome arise because most proteins seem to be processed and modified in complex ways and can be the products of differential splicing;
      • in addition; protein abundance spans a range estimated to be 5 to 6 orders of magnitude in yeast and 10 orders of magnitude in humans.
    • MS analysis
    • MS analysis
    • Two-hybrid analysis
    • Interaction maps - Grid
    • Goals- Aebersold
      • Convergence between discovery science and hypothesis-driven science
      • Systems biology approaches will detect connections between broad cellular functions and pathways that were neigher apparent nor predictable.
      • Ability to collect data already outstrips our ability to validate, integrate, and interpret it.
    • challenges
      • Complexity – some proteins have >1000 variants
      • Need for a general technology for targeted manipulation of gene expression
      • Limited throughput of todays proteomic platforms
      • Lack of general technique for absolute quantitation of proteins