Major biomedical discoveries have been made possible with advanced 'omic technologies, and continued technological advances in 'omic technologies are essential for a more complete physicochemical phenotyping (qualitative and quantitative characterizations) of normal and perturbed biological systems. Biological systems are overwhelming complex, and relatively subtle perturbations in the physicochemical status of these systems clearly lead to profound changes in the health of the organism. The Duke Proteomics Facility (DPCF) is tasked with supporting the protein/peptide characterization needs of the seven Basic Science Departments and the eleven Clinical Sciences Departments of the School of Medicine. The DPCF provides capabilities for mass spectrometry based proteomics for protein identification and protein quantitation, with the wide scope of capabilities required t support a variety of basic science studies and the significant scale of capacity to support clinica studies, specifically including biomarker discovery and biomarker verification experiments. The DPCF has ~ $5,000,000 in dedicated analytical and informatic hardware/software, and a staff of 7 (5 with PhDs, 6 of 7 full time staff). The DPCF has the pipeline technologies critical for LC/LC/MS/MS analysis of cellular proteins and peptides, including a robust and semi-automated analysis pipeline for proteomic, phosphoproteomic and acetylomics studies. In order to more completely physiochemically phenotype phosphoproteomes and acetylomes, the DPCF needs both additional state-of-the-art capabilities and increased capacity, both of which would be provided by the proposed electrospray ionization high resolution, accurate mass tandem mass spectrometer (Q-Exactive, Thermo Scientific). Analyses of identical samples in the DPCF and on a Q-Exactive show the requested instrument provides ~9X increase in coverage of the acetylome and ~ 7X increase in coverage of the phosphoproteome (at the PTM-modified peptide level). Coupling an existing multidimensional nanoscale capillary ultraperformance UPLC/UPLC system (Waters NanoAcquity with Multidimensional Technology) in the DPCF and the requested tandem mass spectrometer (Q-Exactive) will provide the absolute state-of-the-art in instrumentation for phosphoproteomic and acetylomics analyses. The research projects enabled by this proposal will advance our understanding of mechanisms of disease and drug therapy in areas including neurology, oncology, sickle cell disease, infectious diseases, and metabolic diseases. Ultimately, the instrumentation will improve clinical trials and patient therapies through the discovery and characterization of protein 'biomarkers'of health/disease/drug response. The requested system will provide unique performance capabilities that are synergistically aligned with the existing proteomic analysis systems and the comprehensive, dedicated informatics infrastructure in the DPCF, enabling Duke to leverage to the fullest extent the extensive expertise, robust data analysis capabilities, and plethora of important NIH- funded biomedical research opportunities at Duke.
This research proposal will significantly increase both the capacity and the capability of the Duke Proteomics Core Facility to conduct differential expression phosphoproteomic and acetylomics analyses of biological materials in support of a wide variety of NIH-funded biomedical research projects. The research projects enabled by this proposal aim to advance our basic understanding of mechanisms of disease and drug therapy in the areas including oncology, heart disease, liver disease, metabolic disease and infectious diseases, and ultimately the instrumentation will improve clinical trials and patient therapies through the discovery and characterization of protein 'biomarkers'of health and disease. This analysis system will provide unique performance capabilities which are synergistically and complementary aligned with the existing proteomic systems and the comprehensive, dedicated informatics infrastructure in the Duke Proteomics Core Facility, and it will enable Duke to leverage to the fullest extent the extensive expertise, robust data analysis capabilities, and plethora of important biomedical research opportunities at Duke.