Proteomics is the branch of bioinformatics that studies the proteome - the entire set of proteins expressed by an organism's genome. The impetus behind the study of proteomics is the growing understanding that genetics can only explain part of an organism's biochemical interactions. Proteomics is the "next step" to achieve a fuller understaning of the everyday activities of the body, the progression of diseases, and the course of the life cycle.

The differences between the proteome and the genome of an a organism are significant. While the genome of an organism is relatively stable over time, it turns out that the organism's proteome is constantly changing through biochemical interactions both with and away from the genome, such that a single organism can have dramatically different protein expression in different parts of the body or at different stages in its life cycle. Indeed, one of the unexpected discoveries of the Human Genome Project was that while the human genome consists of approximately 33,000 genes, there are approximately 200,000 proteins in the human proteome, and potentially millions if protein fragments and variants are considered.

The explanation for the difference in the number of genes and proteins is a process called post-translational modification, in which functional groups of carbohydrates, lipids, phostphates, and acetates are added to a protein after it's translation from the geneome. This process plays a crucial role in determining the functioning of the proteins, but is not directly coded by the genome. Thus, understanding the genome alone does not provide a complete picture of protein proliferation, structure, and activity.

Current projects to map human and other proteomes are proving vastly more difficult than the mapping of genomes. Not only are there so many more proteins than genes, but whereas the genome is essentially two-dimensional, involving pairs of nucleic acids, and is thus much easier to map and catalogue, proteins are three-dimensional and structurally much more complex, require much more advanced tools to map and more complicated databases to catalogue. Nevertheless, the the potential medical benefits of understanding the proteome are correspondingly greater, and work is pressing ahead on mapping the human proteome at hundreds of institutions worldwide, aided by cooperative and coordinating efforts of umbrella groups such as the Human Proteome Organization (HuPO).

Important tools in the study of proteomics include two-dimensional electrophoresis (2DE) to separate proteins from other bodily materials, peptide mass fingerprinting, mass spectrometry, X-ray crystallography, and NMR to identify and characterize proteins, and most fundamentally, public and collaborative databases of previous and concurrent genomic and proteomic findings to speed up and prevent the wasteful duplication of proteomic research.

Potential applications of proteomic research include the use of protein markers to diagnose disease or measure the efficacy of treatment, and eventually the possible targeting of protiens as a site of theraputic intervention if they are found to play a causal or exacerbative role in the progression of disease.

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