The Proteomics Shared Resource at Burnham Institute offers a state-of-the-art infrastructure for protein analysis at a global level that is tailored to the specific needs of Cancer Center investigators. The core technologies include methods for upfront sample fractionation and back-end protein identification by mass spectrometry (MS) and database searching. Facility MS instruments include Thermo LTQ and LTQ Orbitrap systems, and Bruker HCTUItra and MALDI Autoflex II TOF/TOF systems. Routine services include protein/peptide molecular weight determination by MALDI-MS, differential 2D-PAGE analysis of low to moderately complex samples, identification of gel separated proteins by tandem MS, and post-translational modification mapping for known peptides and proteins. More recently added services include analysis for complex protein samples by multidimensional liquid chromatography (MD LC-MS/MS), phosphoproteomics using 2D or 3D LC-MS/MS methodology, targeted quantitative proteomics employing isotope-labeling strategies (ICPL/ITRAQ/TM), and differential quantitative analysis of complex samples using label-free strategies. Cancer Center investigators are utilizing these technologies in a variety of ways, but most frequently to identify novel components of protein complexes and protein-protein interactions, to map functionally important post-translational modifications such as phosphorylation and ubiquitylation, and to comprehensively profile quantitative differences in protein abundance in cancer versus normal cells. To facilitate these projects, facility personnel routinely meet and interact with investigators to provide guidance with project design, samples preparation, and data analysis. In addition, the facility entertains a rich portfolio in outreach activities geared toward training investigators and their associates in proteomic technology. The facility's future activities will focus on maintaining high quality services as well as the exploration, testing, and demand-based implementation of novel technologies that will benefit the Center's research programs. Efforts in planning toward these goals include promoting additional technologies for accurate quantitative protein profiling in the low abundance range (SILAC), enhancing data analysis, data management and biological interpretation (pathway analysis), and expanding the facility's personnel and instrumentation capacity to a high resolution, high sensitivity mass spectrometry based proteomics facility. In the past year, 25 Cancer Center members used the Proteomics Shared Resource. The requested CCSG support in the first year of $168,553 is 16.6% of the total projected annual Proteomics Shared Resource budget.

Public Health Relevance

Cancer is thought to arise from the accumulation of a series of somatic mutations. However, the genetic make-up as well as mRNA profiles are incomplete descriptors of the malignant phenotype, since proteins are the ultimate executioners of cellular functions. Proteomics provides complementary analytical solutions for deciphering protein functions that are geared toward a systems-level understanding of the cancer phenotype.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
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Subcommittee G - Education (NCI)
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Sanford-Burnham Medical Research Institute
La Jolla
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