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2006 Scientific Report

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Van Andel Research

Van Andel Research Institute | Scientific Report Protein expression As mass spectrometry instruments and protein separation methods develop, proteomics techniques allow researchers to identify and quantitate protein samples of increasing complexity. The ultimate goal is to catalog all proteins expressed in a given cell or tissue, as a means of evaluating all of the physiological processes occurring within. This approach, termed systems biology, aims at understanding how all proteins interact to effect a biological outcome. Traditionally this has been done using 2D gel electrophoresis, image analysis of stained proteins, and identification of proteins from gels using mass spectrometry. Due to the labor-intensive nature of 2D gels and the underrepresentation of some classes of proteins (such as membrane proteins), the field of proteomics has been moving toward solution-based separations and direct mass spectrometry. To that end, our laboratory recently purchased and installed a Waters Corporation Protein Expression System for non-gel-based protein expression analysis. This system represents a paradigm shift in the field of proteomics because it provides both quantitative and qualitative data on complex mixtures of proteins in a single LC–MS analysis. To perform this analysis, proteins are enzymatically digested using trypsin and, without any chemical or isotopic labeling, the resulting peptides are analyzed by LC–MS. The combination of molecular mass and LC retention time establishes a signature for each peptide and allows comparison across samples. The mass spectrometer signal intensity of each peptide is used for quantitation. Qualitative protein identification data is obtained by fragmenting all peptides eluting into the mass spectrometer, a feature unique to the Waters instrument. This system at VARI puts us in an elite group of institutions that have this powerful new technology; fewer than 20 Protein Expression Systems of this type are in operation worldwide. This system will be used to map protein changes under a systems biology approach and to discover biomarkers for early detection and diagnosis of cancer and other diseases. 16 External Collaborators Gary Gibson, Henry Ford Hospital, Detroit, Michigan Michael Hollingsworth, Eppley Cancer Center, Omaha, Nebraska From left: Davidson, Johnson, Cavey Core Technology Alliance (CTA) This laboratory participates in the CTA as a member of the Michigan Proteomics Consortium (MPC).

VARI | 2006 Nicholas S. Duesbery, Ph.D. Laboratory of Cancer and Developmental Cell Biology Dr. Duesbery received both his M.Sc. (1990) and Ph.D. (1996) degrees in zoology from the University of Toronto, Canada, under the supervision of Yoshio Masui. Before his appointment as a Scientific Investigator at VARI in April 1999, he was a postdoctoral fellow in the laboratory of George Vande Woude in the Molecular Oncology Section of the Advanced BioScience Laboratories–Basic Research Program at the National Cancer Institute–Frederick Cancer Research and Development Center, Maryland. Dr. Duesbery was appointed Deputy Director for Research Operations in March 2006. 17 Staff Laboratory Staff Philippe Depeille, Ph.D. Yan Ding, Ph.D. Hilary Wagner, M.S. John Young, M.S. David Slager, B.S. Elissa Boguslawski Students Students Chia-Shia Lee, M.S. Lisa Orcasitas Zafar Qadir Visiting Scientists

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