Sequencing the genome established a firm foundation—but proteomics is the next, more difficult phase in the process of understanding cellular biochemistry and mechanisms of disease. Since the term “proteome” was coined in 1994 by an Australian graduate student, it has come to be used and defined in a variety of different ways. We define it as follows:

The identification, characterization and quantification of all proteins involved in a particular pathway, organelle, cell, tissue, organ or organism that can be studied in concert to provide accurate and comprehensive data about that system.

In other words, if the genome represents the words in the dictionary, the proteome provides the definitions of those words. Then, the patterns of how these proteins interact with each other, with their environment, and with other molecules provide the grammar and syntax to form meaningful language. It is these interactions that define an individual’s state of wellness or disease. For example, a specific configuration of proteins in liver tissue could define a particular tumor, or a successful regression of that tumor, in response to therapy.

To create the best drug for any disease we have to pick the best target. To do this, we must define all of the forms that an individual protein can take, all of the other proteins it can touch, and all of the pathways in which it can participate. Proteomics depends on the development of comprehensive, high-throughput methods to look at all of the forms of all of the proteins with which a potential protein therapeutic, small molecule drug or protein target can interact. With earlier methods, we could only look at one effect at a time. Proteomics allows us to look at hundreds or thousands of protein interactions at the same time.

When scientists can accurately and dependably identify and understand the activity of these protein systems, we will be significantly closer to understanding the underlying characteristics of disease and wellness. Thus, proteomics has the potential to revolutionize the development of innovative clinical diagnostics and pharmaceutical therapeutics.