Proteomics and Metabolomics

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Proteomics and Metabolomics Shared Resource-Stephen Byers, PhD /Albert Fornace, Jr, MD The mission of the Proteomics and Metabolomics Shared Resource (PMSR) is to provide state-of-the-art tools, methods, and mass spectrometry-based technology to investigators. This centralized shared resource is available to researchers for routine and specialized proteomic and metabolomic applications. The aim of PMSR is to provide an 'in house' resource, rich in technical expertise that fosters the free flow of experimental knowledge and collaborations across the Lombardi Comprehensive Cancer Center (Lombardi). The PMSR offers an array of proteomics- and metabolomics-based services. It is equipped with two-dimensional (2D) gel electrophoresis apparatus including DIGE imager and spot picker (GE Healthcare), 4800 MALDI TOF-TOF instrument (ABI), and a QSTAR Elite Hybrid LC MS/MS system (ABI) to support the proteomic workflow. Each instrument has the latest integrated software and database search engines (e.g.. Protein Pilot, GPS explorer) for protein identification and data processing. In addition, PMSR houses a QTOF Premier (Waters Corp.) online with an UPLC system for metabolomic profiling and drug metabolism studies. The data processing for metabolite biomarker studies is supported by the 'SIMCA-P' and the 'Random Forest software'. PMSR also manages a 4000 QTrap, which supports quantitation and validation for small-molecule metabolites, and allows targeted proteomic analysis. PMSR staff includes a dedicated bioinformatician who works closely with the Biostatistics and Bioinformatics Shared Resource (BBSR), as well as with the Georgetown University-based Protein Information Resource (PIR). The most common experiments include identification of proteins contained in bands/spots isolated from electrophoretic gels, as well as comparative proteomics using shotgun and stable isotope labeling strategies. The high speed, sensitivity, and accuracy of our mass spectrometry experiments allow accurate qualitative and quantitative proteomics. The metabolomics initiative has been driven by Dr. Albert Fornace, Jr, and involves UPLC-TOFMS based biomarker discovery for radiation exposure. This technology is now available to investigators for their specific research interests. Written and electronic reports are provided for all samples, and the average turn-around time is two weeks. The PMSR is able to carry out experiments that detect and characterize protein modifications such as phosphorylation and acetylafion. These experiments are challenging and require a more intensive effort. However, the combination of the complementary mass spectrometric methods available in PMSR, staff expertise and experience, and the ability to work closely with investigators, have allowed the successful completion of a number of these difficult projects. The PMSR was established in January 2006 and has grown dramatically, both in resources and use. Lombardi has invested over $1 million in equipment alone for the PMSR; as a result, the facility consistently provides high quality data to many investigators from 5 programs within Lombardi. The PMSR is run under the directorship of Drs. Stephen Byers and Albert Fornace Jr.