Shared Resources Core 2: Quantitative Proteomics Core

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Project Summary The Quantitative Proteomics core led by Dr. Benjamin Garcia will provide cutting-edge mass spectrometry (MS) based proteomics technologies to the P01 Project team members to help elucidate biochemical mechanisms involved in histone and histone-like mutations in human cancers. These MS approaches will include quantitative experiments to understand protein expression and post-translational modifications (PTMs) on histone and non-histone proteins from both cultured and primary cell lines, tissue/tumors and formalin fixed paraffin embedded (FFPE) archived samples. Although most researchers in the epigenetics and chromatin biology fields utilize antibody based methods for histone modification characterization, antibodies have many technical issues (such as epitope occlusion), which confound the analyses. Mass spectrometry therefore provides a more unbiased and complementary approach, that is also more sensitive and accurate for protein PTM analysis. The Garcia Lab has for over a decade now developed methods for histone PTM analyses. Here in this propose we plan to continue to expand our proteomics toolbox to allow P01 team members to be able to characterize 500 histone PTM sites in rapid fashion, perform quantitative analyses of histone combinatorial modifications, and determine which oncogenic histone mutations affect chromatin structure. Additionally, we will explore the downstream protein signaling pathways that are altered in epigenetically driven human cancers, as transcriptional profiles do not always provide the most accurate pictures of protein expression. !