Proteomics For any given species, the space of possible biomolecules and their organization into pathways and processes is large but finite.
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?
Antibody arrays Good for low-abundance proteins Problem is antibody specificity
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.
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