The Biomedical Mass Spectrometry and Proteomics Resource Center, is supported by the Adelson Medical Research Foundation, UCSF-, HHMI- and NIH-funded instrumentation and biological research project grants. This Resource Center provides leadership, expertise and advice about proteomic methodologies to investigators and their groups on the design and implementation of suitable experimental strategies that will enable them to achieve their research goals. The Resource staff then carries out the experiments and the processing of the data sets obtained, and works with the students, postdocs and faculty on interpretation of the results.
The Center’s faculty and staff conduct collaborative research focused on a wide variety of challenging problems involving the human and related proteomes and their dynamics. Active project areas include neurobiology, cell biology, biomedical projects, cancer signaling and in plant proteomics. The Center is a world leader in facilitating proteomic analyses per se as well as in the development of better methodologies to enable studies of new problem areas in parallel.
One major research area focuses on the global analysis of post-translational modifications in many cell and tissue systems, including phosphorylation, O-GlcNAcylation, ubiquitinylation, etc. and development of mass spectrometric methods for quantitative comparative analysis of protein and post-translational modification levels and dynamics, e.g. applying PRM and neucode MS. Another major area involves the characterization of protein-protein interactions and protein complexes using affinity and proximity proteomics strategies. Finally studies of the architecture of very large protein machines are on-going using high sensitivity chemical cross-linking, peptide sequencing mass spectrometry and cryoEM studies.
Center instrumentation includes several Orbitrap-based mass spectrometry platforms including the XL, Velos, Q-Exactive Plus, Elite, Fusion-Lumos and an ion-mobility Exploris 480 systems and associated capillary liquid chromatography systems.
The Center also continues to develop and support one of the leading suites of tools for analysis of large mass spectrometry-derived proteomics data, Protein Prospector. Current web-based releases allow unrestricted searching of MS and MSMS data, by the research community, as well as the ability to perform comparative quantitative analysis of samples using isotopic-labeling reagents. It allows comparative assessment of individual MS2 spectra using MS-Viewer. It is the only freely-available web-based resource that allows these types of comprehensive analyses.