This competitive renewal requests continued funding of the national Bio-organic, Biomedical Mass Spectrometry Resource Center located at the University of California, San Francisco new Mission Bay campus. Challenging problems of scientific, translational and clinical importance originating outside of the resource itself drive the development and evolution of core methodology, technologies and software tools toward integrated and optimized workflows. In addition the resulting enhanced capabilities of these resource experimental strategies and experience benefit many other broad areas of collaboration directly. As a general theme this Resource is focused on gaining a detailed molecular understanding of the mammalian proteome, its dynamic covalent modulation by endogenous stimuli and exogenous agents such as drugs, drug candidates and infectious agents, and finally studies of molecular defects underlying human diseases. Resource activities include (1) the sequence determination and identification of new proteins involved in protein machines, assemblages, complexes and organelles, (2) the characterization of posttranslational modifications that address questions about how protein function is modulated and regulated, (3) issues of multiple posttranslational modifications that may function synergistically, and (4) the dynamics of reversible posttranslational systems. Particularly in the last few years the tools of chromatography, affinity chromatography and advanced ion optical systems are poised with unprecedented analytical power to address posttranslational and epigenetic complexity directly. Among the many other tools required to meet Resource obligations, we propose integration and optimization of high sensitivity workflows based on larger polypeptides and the second generation electron transfer (ET) Orbitrap platform to address multiple posttranslational occupancies and simplify digest mixtures; for example, to open new lines of inquiry such as studies of phosphorylation and O-GlcNAcylation together, nucleosome-level histone occupancies, etc. Biodriver topics include: autism, Alzheimer disease, apoptosis and inflammation, chemotherapy biomarkers, parasitic diseases, stem cell and chromatin-templated processes including cancer, and neuronal organelles and axon regeneration.