One of the most dramatic current developments in biological research is the shift from the analysis of single genes and proteins to the comprehensive analysis of biological systems and pathways. This shift is a consequence of the development of automated, high throughput genomic technologies and their application to sequence complete genomes and to measure gene expression on a genome-wide scale. Currently, no comparably powerful technology is available for the analysis of biological systems on the protein level. Howe er, proteins are the most significant class of biological effector molecules, and a complete model of a biological process cannot be established without knowledge of the identify, function and state of activity of the proteins involved. The work proposed in this application is aimed at the development of a technology for the rapid, sensitive, quantitative and comprehensive analysis of protein expression profiles in complex biological samples, ultimately in whole cell lysates. Once developed such a technology will be an essential tool for biologists' attempts to interpret the linear information of genomes in terms of function, control and mechanisms of biological systems.