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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