PROTEOMICS CORE

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Proteomics, as one of the evolving disciplines of the "omics" cascade (genomics, transcriptomics, proteomics and metabolomics) is projected to have a profound impact on the clinical practice of gastroenterology and hepatology in the coming decades (Lazaridis et al., 2005). Within the past five years, the advances in proteomics have been hallmarked by orders of magnitude increases in speed and sensitivity of data acquisition that is driving bioinformatics efforts for data interpretation and integration into the "omics" pipeline. The "data gathering" technologies for proteomics now have a firm, quantitative foundation (Feng et al., 2008). The integration of all "omics" data from the same high quality human samples is a fundamental step for the application of high-dimensional biology to preventing, diagnosing and treating Gl disorders, and is one of the imminent challenges. As discussed below under 'D. Bioinformatics and Data Integration' the assembly of proteomics data with other 'omics' data and clinical information is a major goal of the DDRCC Proteomics Core. Since the last competitive renewal, the Proteomics Core Laboratory has evolved to incorporate the most advanced technologies and software into novel, comprehensive workflows for DDRCC investigators, as detailed below. With the support of the CTSA, the Core has added staff scientists to provide DDRCC investigators the expertise and assistance to design and interpret statistically sound and cost-effective complex clinical proteomics experiments. The Core has pioneered new methods of sample processing and analysis such that proteomics and functional genomics data can be generated from the same samples that have been procured from tissues of patients with inflammatory bowel diseases (see Preliminary Results and Rader etal., 2008). The cost effectiveness of the Proteomics Core extends to the capital-intense requirements of proteomics analyses. The DDRCC resources are insufficient to support an independent unit. With increasing capacity demands for the analysis of clinical samples, the Proteomics Core has initiated and supervises an intramural mass spectrometry consortium that provides 24/7 advanced mass spectrometric analysis of proteins, peptides and metabolites in clinical samples (see Figure 17). The Proteomics Core serves as a central institutional core and is also supported by the National Institutes of Health, National Centerfor Research Resources (UL1-RR024992 (Kenneth Polonsky, Pl)'and P4r-RR000954 (Michael Gix)ss, PI), National Cancer Institute (P30 CA91842, Tim Eberlein, PI), the W. M. Keck Foundation, the Siteman Cancer Center, and other institutional resources. By subscribing to this central facility and supporting the salaries of the highly qualified staff required to carry out proteomics experiments, the DDRCC can offer its members services at a discounted price that covers only the price of supplies and reagents.