Proteomics is an exciting discipline in its infancy that means different things to different people. It is also a field limited by the technologies currently available to its practitioners. Important questions arise: How can we usefully define proteomics? Which research questions offer the greatest promise for the field? What new tools will be needed to pursue those questions?

Perhaps the most appropriate definition of proteomics is "any large-scale or systematic characterization of the proteins present in a cell, tissue, or organism." It is a different paradigm from conventional reductionistic scientific investigations that typically focus on a single gene or protein. Proteome research asks unbiased biological questions such as what protein levels or activities change between two experimental conditions.

Although sequencing the human genome was initially daunting, it was a finite problem with a specific endpoint. In contrast, the proteome of any organism is highly dynamic with an endless number of...

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