Driven by technological advances and investigator demand, this Core has evolved from the previous goal of providing DNA microarray, proteomics and metabolomics services all in a single integrated Core to a core specialized on proteome responses. To most efficiently utilize available resources it was decided to contract out DNA microarray services and consolidate the metabolomic services into Core A (Analytical Chemistry Core) while focusing on Proteomic Services in Core B. The Core will develop and provide workflows for proteomics services including profiling of complex protein mixtures (with protein separation and mass spectrometric identification), analysis of posttranslational modification (PTM), including phosphorylation, thiol oxidation, ubiquitination, and activity-based protein profiling of proteases (caspases, etc.). In conjunction with Core A (Metabolomics), the Core will also implement post-MS bioinformatic analyses to enable efficient and comprehensive processing, archival, and utilization of proteomic data sets. Experimental approaches practiced in this core will be based on two-dimensional (2D) separation of complex protein mixtures by 2D gel electrophoresis (2DGE) and 2D liquid chromatography (2DLC). Fractionated mixtures will be analysed by three different mass spectrometry approaches: (i) analysis of trypic in gel digests from 2D gel spots and (ii) analysis of complex peptide mixtures prepared by in-solution trypsin digestion by (iia) offline LC-MALDI MS/MS or (iib) online LC-MS/MS. Proteomic datasets generated by these experimental approaches will be used for protein identification quantitative protein profiling, and PTM analysis. In collaboration with core A, the Core will also provide analytical support for storage and access of proteomics data. Additional integrating themes with other cores will be to find characteristic responses of human and other organisms to given agents, identifying biomarkers of early response, and finding no effect levels for the most sensitive biomarkers of effect. The emphasis will be on increasing efficiency of resource utilization. Thus, highly trained Core personnel will concentrate their efforts on establishing innovative and robust workflows as well as performing technically demanding functions, providing help for planning experiments, and training Project personnel in conducting their own proteomics experiments where feasible.
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