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Software Solutions to Proteomics Problems

As genome sequencing becomes a regular occurrence, biology's attention can turn to the next logical step: proteomics. Fundamentally, proteomics is nothing less than the complete catalog of every protein in a given tissue, organ, or organism under a defined growth or disease state. Sometimes this definition is expanded to include protein-protein interactions. The data describe the types and quantities of proteins present and also indicate other proteins with which these molecules are complexed.

Bob Sinclair
As genome sequencing becomes a regular occurrence, biology's attention can turn to the next logical step: proteomics. Fundamentally, proteomics is nothing less than the complete catalog of every protein in a given tissue, organ, or organism under a defined growth or disease state. Sometimes this definition is expanded to include protein-protein interactions. The data describe the types and quantities of proteins present and also indicate other proteins with which these molecules are complexed.

Typically, protein identification and quantitation is accomplished by electrophoretic separation of protein mixtures on 2-D gels followed by mass spectrometric analysis of individual protein spots. Interaction data is usually collected using the yeast two-hybrid assay system. Because of the high-throughput nature of proteomics projects, keeping track of and processing all of the data can become a juggling act. Fortunately, scientists conducting this type of research can find software products to assist them every step along the way....

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