Core B: Proteomics and Metabolomics

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Core B Summary The Proteomics and Metabolomics Core (Core B) provides state-of-the-art instrumentation, methodology, and expertise in analytical proteomics and metabolomics to investigators in this PPG. A unique feature of the Proteomics and Metabolomics Core is the availability of cutting-edge quantitative proteomics analysis technologies that allows high sensitivity measurements of proteome changes in models of gastric cancer. New services in this renewal application include discovery and targeted metabolomics as well as tissue imaging mass spectrometry (IMS). The Core provides 1) identification and quantitation of proteins in complex samples, 2) analyses of protein modifications, including phosphorylation, 3) quantitative analyses of metabolite abundances, and 4) molecular imaging of gastric tissue using IMS. Core staff provide consultation on experimental design as well as hands on sample preparation, mass spectrometry analysis and primary data analysis. Multiple high performance mass spectrometers for LC- MS/MS experiments are available for proposed analyses. In addition, advanced methods are available including: multidimensional LC-MS/MS for protein identification from complex samples, TagRecon database searching analysis for identification of unanticipated modifications or sequence variants from MS/MS data, and high spatial and mass resolution imaging methods for tissue analysis. The Core also provides relative quantitation using stable isotope differential labeling strategies, iTRAQ and SILAC, for samples derived from animal models or from cell culture, respectively. Validation of protein expression or metabolite abundance changes is accomplished using targeted multiple reaction monitoring LC-MS/MS methods. Project 1 (Peek) will utilize metabolomics methods to measure metabolite changes in H. pylori strains isolated from infected iron deplete or replete gerbils as a function of time. Project 2 (Wilson) will utilize phospho-SILAC to measure changes in the phosphoproteome and metabolomics to measure metabolite changes in macrophages upon H. pylori infection and with EGFR or DHPS inhibition. Project 3 (Cover) will employ metabolomics methods to examine metabolite changes in plasma and gastric tissue. In addition, this project will utilize IMS methods to measure changes in metabolites, proteins and lipids in gastric tissue in a spatially- resolved manner as a function of dietary salt, infection and inflammation. !