Proteomics is the systematic identification and characterization of the proteins (the proteome) of a cell, tissue, or organelle (reviewed in PANDEY and MA”, 2000). The study of global gene expression using microarrays or SAGE is reliant on the observed phenotypic changes being the result of dynamic changes in particular mRNA populations. Although extremely powerful, these types of analyses attempt to simplify the relationship between genes and their protein products, which are in fact the active agents in the cells. A complementary approach is proteomics. Through the application of 2-D gel electrophoresis, which separates proteins based on their charge and mass, thousands of proteins can be analyzed at one time. Each protein can be identified through a combination of microsequencing using mass spectrometry and bioinformatics.
This allows the identification of the primary gene products and their post-translational modifications. These new technologies are allowing researchers to identify numerous novel proteins controlling important biological processes, including plant proteins expressed in response to drought, anoxia, and other environmental changes (reviewed in Z I V Y and DE VIENNE, 2000). Proteomics has also been applied to the study of mutant lines, allowing the analysis of both the direct and indirect consequences of metabolic changes caused by a single gene mutation.
It is unlikely that the differential display techniques, which utilize this combination of 2-D electrophoresis and mass spectrometry, will ever surpass the sensitivity of microarray technology. However, proteomics is not limited to the study of expression patterns, but also encompasses high-throughput functional biochemical analyses of the proteome. By elucidating protein-protein interactions using mass spectrometry and the yeast-two-hybrid system it is possible to gain insight into the functions of many unknown proteins. For example, the yeast two-hybrid system has been used to identify plant proteins which interact with viral proteins upon infection of a plant. This work is beginning to elucidate the mechanisms by which the plant recognizes and prevents the replication of invading viruses.