In this presentation we will discuss a new approach to quantitative proteome analysis and show results from selected applications of the technology to microbial and mammalian cell systems. The technology is based on a new class of chemical reagents termed isotope coded affinity tags (ICAT) (Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R, Nature Biotechnol 1999; 17:994-9). The reagents and the tandem mass spectrometry-based analytical process allow the precise quantitation and identification of large numbers of proteins in complex mixtures rapidly and sensitively. The need to separate and analyze extremely complex peptide mixtures challenges the separation sciences. Optimized peptide separation protocols connected on-line with mass spectrometers will be discussed. The applications will document the performance of the method to examine changes in protein profile in yeast cells induced by metabolic shifts, to measure quantitative differences in the cell surface protein profile in mammalian cells, and to detect and quantify changes in protein phosphorylation profiles in cell lysates.
Current applications of quantitative proteomics technology at the Institute for Systems Biology are directed towards the discovery of proteins markers that differentiate cancer cells from their normal counterparts, to the investigation of the mechanisms of fundamental cellular processes by the comparative analysis of the gene and protein expression profiles in cells at different states, and to studies in the area of medical microbiology.
Dr. Aebersold completed his undergraduate studies in biology at the University of Basel, Switzerland in 1979 and received a Ph.D. in cell biology at the Biocenter of the University of Basel in 1984. Holding fellowships from the Swiss National Science Foundation and EMBO he joined the California Institute of Technology as a postdoctoral fellow (1984-86) and remained at Caltech as a senior research fellow (1986-88). In 1988 he joined the University of British Columbia in Vancouver as an assistant professor in the Department of Biochemistry and Molecular Biology and as a senior investigator at the Biomedical Research Centre. In 1993, he moved to the University of Washington as an Associate Professor in Molecular Biotechnology and was promoted to full Professor in 1998. He served as the Associate Director for the Science and Technology Center for Molecular Biotechnology from 1994-2000. In 2000, he left the University of Washington and joined the Institute for Systems Biology as co-founder and full faculty member.
Dr. Aebersold is a senior editor for the journal Physiological Genomics, has been a member of the Editorial Advisory Boards of Protein Science (1992-'98), Functional Proteomics (1999- present), Analytical Biochemistry (1991-present) Functional and Integrative Genomics (1999-present) and Electrophoresis (1989-1993).