Integrative and Quantitative Mass Spectrometry (IQ-MS): Developing a unified sample workup for multi-omics analysis

Cancer, or the rewiring of biological cells for unabated proliferation, is a disease comprising of dysregulated, complex macromolecular networks. To better understand the heterogeneity of cancer and the spectrum of response to drug therapies, multiple quantitative “omics” datasets, or multi-omics, are generated and analyzed. This dissertation chronicles the development of our multi-omics platform from simple in vitro tissue culture to more complex in vivo subcutaneous tumors. In each chapter, we utilize a global bottom-up proteomics and phosphoproteomics approach to explain metabolic and phenotypic changes highlighting critical mediators of sensitivity or resistance to the studied perturbations. This approach reveals rationally-designed combination therapies which produce synthetic lethality that are translated to in vivo tumor models. Also discussed is the current state and future of our multi-omics platform. This platform generates multi-omic datasets from single tumor homogenates with automated sample workup. Our future goal is for a comprehensive, site-specific analysis of multiple post-translational modifications including phosphorylation, intact glycosylation, reversibly-oxidized cysteines, and nitrotyrosines using novel cysteine- and amine-reactive probes functionalized with phosphonic acid for selective enrichment via immobilized metal affinity chromatography