Structural Characterization of Polypeptides, Protein Complexes, Oligosaccharides

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DESCRIPTION (provided by applicant): The UCSF Sandler-Moore Mass Spectrometry (SMMS) Core Facility proposes acquire a Synapt HDMS instrument in order to apply ion mobility separation (IMS) technology to enable high specificity tissue imaging and advanced structural studies on various classes of biomolecules, (e.g., peptides, proteins, protein complexes, oligosaccharides and lipooligosaccharides). We seek funding to purchase a Waters Synapt HDMS system which offers a unique combination of capabilities currently not matched by other instruments on the market. This acquisition will benefit investigators from the UCSF campus as well as our neighboring research institutions with whom we maintain close collaborations: the San Francisco Veterans Affairs Medical Center, UC Berkeley and the Buck Institute for Age Research. Our long-term objective is to broaden the scope of mass spectrometry-based services that our core facility offers to include two new areas: (1) mass spectrometry of large biomolecules in their native state and their non-covalent assemblages, (2) high definition MS-based tissue imaging, and (3) we want to enhance our current capabilities in structural characterization of medium size molecules (e.g., peptides, lipids, oligosaccharides) within complex matrices by adding an additional stage of separation afforded by an IMS mass analyzer. Furthermore, the MS(e) technology that allows for increased sampling efficiency in MS/MS experiments makes the Synapt HDMS instrument an attractive tool for proteomic studies that our facility routinely performs. Mass spectrometry of biomolecules in their native state complements the classical, optical detection-based techniques of higher order structure characterization. Specific aims in the area of native mass spectrometry include implementation of known protocols and development of new methods for MS-based elucidation of composition, stoichiometry, architecture and collision cross section of protein complexes and protein-ligand assemblages. Availability of well characterized heteromeric protein complexes as models (e.g., septins) will allow us to validate our protocols before applying them to target studies that are outlined in this proposal. Importantly, we will work closely with Dr. Evan Williams from UC Berkeley who is an expert in the field of gas-phase ion chemistry and a contributing Co-Investigator on this application. A second set of aims addresses our plans to establish a robust method for analysis of small molecule spatial distributions (< 4 kDa) in tissue biopsies. We will not only map but also identify the species of interest, a realistic goal in view of the documented capabilities of the Synapt HDMS in this area. Finally, we will address the need for identification and characterization of species of similar structures that are present in complex mixtures at variable concentrations. To this end, we will take advantage of IMS to facilitate analysis of minor components with overlapping m/z values, including structural isomers. In conclusion, the Synapt HDMS will support a variety of basic and translational research studies directly relevant to cancer, reproductive and endocrine disorders and bacterial infections. PUBLIC HEALTH RELEVANCE: Detailed characterization of the structure and function relationships among various components of a living cell is a foundation of any research aiming at understanding pathophysiology of disease, developing cures and offering preventive measures. Waters Synapt HDMS system offers a versatile combination of technologies that enable structural characterization of very large "molecular machines" as well as small molecules, all responsible for the maintenance of a well balanced biological system. We will use this instrumentation to support studies on cancer, reproductive and endocrine disorders and bacterial infections.