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2009 Scientific Report

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Van Andel Research

Van Andel Research Institute | Scientific Report Gregory S. Cavey, B.S. Laboratory of Mass Spectrometry and Proteomics Mr. Cavey received his B.S. degree from Michigan State University in 1990. Prior to joining VARI he was employed at Pharmacia in Kalamazoo, Michigan, for nearly 15 years. As a member of a biotechnology development unit, he was group leader for a protein characterization core laboratory. More recently as a research scientist, he was principal in the establishment and application of a state-of-the-art proteomics laboratory for drug discovery. Mr. Cavey joined VARI as a Special Program Investigator in July 2002. Staff Paula Davidson, M.S. Caryn Lehner, M.S. Matthew Welsh, B.S. Debra Guthrey 14

VARI | 2009 Research Interests Mass spectrometry–based proteomics is now an important and widespread tool in basic and clinical research. In 2005, VARI purchased a Waters quadrupole time-of-flight (Q-Tof) mass spectrometry system that remains at the cutting edge of many research applications. This equipment allows us to provide routine mass spectrometry services and to develop new services such as protein profiling for biomarker discovery and protein phosphorylation analysis. Protein identification and protein molecular weight determination are routine services performed on sub-microgram amounts of material to address a wide variety of biological questions. Protein identification via mass spectrometry is mainly used to identify novel protein-protein interactions and can be performed on proteins in SDS-PAGE gels or in solutions. Molecular weight determination of protein solutions is typically used to confirm the expression and purification of recombinant proteins to be used as reagents in x-ray crystallographic experiments or drug screening/cell-based assays. Our research emphasis is on 1) developing liquid chromatography–mass spectrometry (LC-MS) protein profiling analysis for systems biology research and biomarker discovery and 2) improving methods for identifying and quantifying the phosphorylation of proteins. LC-MS protein profiling Our lab collaborates with Waters Corporation, a major manufacturer of mass spectrometry and HPLC equipment, to evaluate and improve existing methods while applying LC-MS to the research efforts of VARI scientists and of external clients. Our LC-MS system employs a novel data acquisition method unique to Waters mass spectrometers, termed LC-MS E , whereby quantitative and qualitative data are collected in a single analysis. Protein samples are first digested into peptides using trypsin and then analyzed by reverse-phase nanoscale LC-MS. Recording peptide mass, HPLC retention time, and intensity as measured in the mass spectrometer, we digitize the data to allow comparisons across samples. Quantitation is based on measuring and comparing the chromatographic peak area for each peptide across samples. Qualitative protein identification data is collected in a multiplexed, non-intensity-biased fashion concurrent with quantitative data. One current pilot project is a time-course analysis of protein secretion (secretome) from mouse 3T3-L1 pre-adipocytes as they differentiate in response to treatment with dexamethasone/insulin, versus the response to the PPARg antagonist rosiglitazone. A second study is of the secretome of a cell line model of cachexia. In addition to mechanism-of-action studies, our goal is to use LC-MS to discover candidate biomarkers of disease. Current research efforts focus on sample processing techniques to reproducibly fractionate highly complex samples such as blood plasma, tissue, and urine to allow quantitative analysis. Replicate LC-MS analysis of carefully chosen samples and multivariate data analysis will allow us to differentiate between normal biological variation and disease. Protein phosphorylation analysis Mapping post-translational protein modifications such as phosphorylation is an important yet difficult undertaking. In cancer research, phosphorylation regulates many protein pathways that could serve as targets for drug therapy. In recent years, mass spectrometry has emerged as a primary tool in determining site-specific phosphorylation and relative quantitation. Phosphorylation analysis is complicated by many factors, but principally by the low-stoichiometry modifications that may regulate pathways: we are sometimes dealing with 0.01% or less of phosphorylated protein among a large excess of a nonphosphorylated counterpart. 15

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