Mass Spectrometry is a new core in this renewal of CA140043 that will be used extensively by all three projects. Due to major shifts in research emphasis, it is important to add expertise and high performance mass spectrometry (MS) capacity to address complex proteome analysis problems and provide quantitative analysis of key metabolites. This Core will: assist in experimental design (i), process samples (ii), conduct LCKMS/MS analyses (iii), process the MS data (iv), deliver reports to Core A (biostatistics) and the pertinent Project providing the samples (v), and assist in the biological interpretation of results (vi). Quantitative proteome comparisons will include LCKMS/MS analysis of: isolated protein complexes with and without chemical crosslinking; global analyses of exosomes; and global analysis of purified cells or cell lines. The proteome analyses will use methods and state-of-the-art instruments that can detect and robustly quantify most of the proteins present in complex samples, including whole cell lysates. Quantitative targeted analyses of key metabolites will be conducted using multiplexed MRMKMS on a triple quadrupole mass spectrometer. The Mass Spectrometry Core is complementary to an existing Cancer Center Proteomics Core at the Wistar Institute. The Proteomics Core provides routine proteome analyses, but it does not provide quantitative metabolite assays and it does not perform many of the types of proteomics analyses needed here. Furthermore, the dedication of a full time research scientist to this program project ensures that proteomics and metabolite analyses will be optimally performed in a timely manner. The MS Core will have full access to the Wistar Institute Mass Spectrometry Resource, which is equipped with state-of-the-art instruments. This resource is shared by the MS Core, the Proteomics Core, and Dr. Speicher’s research group. This resource is managed by Dr. Tang, and it has sufficient instrument capacity to avoid significant backlogs. The Specific Aims for this core are: 1) to provide complex proteome analyses using state-of-the-art and innovative methods with high sensitivity, high mass accuracy mass spectrometers and 2) to provide quantitative multiplexed analysis of targeted metabolites using multiple reaction monitoring mass spectrometry (MRMKMS).