Global genome initiatives including the Human Genome Project have generated enormous amounts of information, spurned new technologies and catalyzed the emergence of a new type of biology which attempts to build biological knowledge from the global analysis of biological systems, pathways and cells. In this program we propose to develop a novel technology for the quantitative and global analysis of protein expression profiles in biological samples including biochemical and subcellular fractions, biological fluids, cells and tissues. Thus, this technology will extend the global approach to biological research to the analysis of proteins, the molecules that universally constitute the structure, function and control of biological systems. The basis of the technology is a new class of reagents we term isotope coded affinity tags. The tags which are introduced to specific functional groups in proteins post isolation serve as both, ligands for the isolation of tagged protein segments as well as a quantitative code which can be mass spectrometrically deconvoluted. The proposed program has three distinguishing features which satisfy the request for innovative technology development. First, the technology explores a new approach to quantitative protein analysis and has the potential to become the technical foundation of the emerging field of proteomics. Second, the research will be conducted by a multidisciplinary team constituted as an academic/industrial partnership. This partnership is expected to accelerate dissemination of the technology by developing, commercializing and supporting the required chemistries, instrumentation and software as mature, integrated products. Third, the research will be conducted in a unique research environment, the new Institute for Quantitative Systems Biology at the University of Washington. The structure of this institute embodies the evolution of a technology from its inception to the integration into biological research programs and to the support of large-scale applications. The Institute also provides the interdisciplinary research environment and the facilities required for the academic/industrial partnership to flourish. 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. Applied to cancer research the method will permit the quantitative measurement and identification of the molecules that distinguish a particular cancer cell from a normal cell. The technology will thus significantly contribute to the molecular diagnosis, the assessment of the cancer risk and prognosis, and the understanding of the molecular basis of cancer.