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With the Human Genome Project in its culminating phase, scientists are turning to the task of converting the soon to be completed DNA sequence into information that will improve human medicine and health care. One of the key challenges ahead is understanding how proteins direct biological functions. Proteomics, the science of the cellular protein universe, attempts to catalog and characterize proteins, compare variations in their expression levels under different conditions (i.e., various stages of disease compared with nondisease states), study their interactions, and identify their functional roles. However, these studies will not produce a complete "proteome," or a map of an organism, because cells are always changing, as is protein expression. Scientists believe there is a powerful distinction to be made between the molecular function of an isolated protein and the function of that protein in the complex cellular environment.

The goals of proteomics in medicine are to provide the ability to predict rather than confirm disease and to construct a new, systematic way to discover drugs. A preliminary step in achieving these goals requires that researchers acquire or invent the technology to fit its aspirations. Several approaches are being studied including structural genomics, a branch of proteomics, which studies the shapes of proteins with the goal of constructing a lexicon as well as an understanding of where in the body different proteins are produced, and how each is controlled. One molecular biologist, Richard Burgess of the McArdle Laboratory for Cancer Research at the University of Wisconsin, defines the scope of proteomics as "a grab bag of activities that are all in the postgenomics or functional genomics area, or the what-do-we-need-to-know-to-make-sense-of-all-the-genomics-data arena."

Proteomics is not the study of proteins one by one, as has been done traditionally, but in an automated, large-scale manner that requires new technologies and techniques. Proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and, ultimately, their function. Considerable effort is currently being devoted to the development of novel technologies to unravel the mystery of proteins.

Companies competing in the proteomics space offer technology platforms for discovering or screening drug candidates or diagnostic markers. One of the ways emerging proteomics companies fund their enterprises, is selling their services to the pharmaceutical industry through an wide array of alliances and collaborations. This report will examine competing technologies, and the alliances being formed in the proteomics arena today.

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