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.
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?
Frequently from biochemical analyses
In silico analysis
GFP or other tagging
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
Process for protein isolation
2D gel electrophoresis
Antibody arrays Good for low-abundance proteins Problem is antibody specificity
Array-based protein interaction detection
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.
Interaction maps - Grid
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.
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