Proteome, transcriptome and genome: top down or bottom up analysis?

Biological systems are comprised of protein components found at a wide variety of abundances from millions of molecules of a single species per cell to less than one copy per cell. Because of this wide range of concentrations, measurement or a full accounting of each system is presently unavailable. Conventional separation and analytical methods (two-dimensional gel electrophoresis and mass spectrometry) allow identification and quantitation of many of the most abundant gene products (top down methods); and the majority of gene products, which are found at low abundance, can be neither identified nor measured in complex mixtures at present. The gene products that are found at low levels can be characterized and their properties analyzed by preparing ordered gene libraries of limited complexity from mRNA. When such preparations are expressed in cell free systems and analyzed by two-dimensional gel electrophoresis, the features of the gene products are available for analysis. This 'bottom up' approach allows identification of gene product properties so that analytical procedures can be devised and applied to complex mixtures.