Our lab makes extensive use of mass spectrometry to study the structure and function of enzymes and to profile the chemical complexity of biological systems. As a tool for structural biology, the major advantages of mass spectrometry over other techniques include its sensitivity, its ability to simultaneously inventory multiple ligand bound/oligomeric states, and its ability to profile conformationally dynamic and structurally heterogenous systems in several different modalities. The major limitation of mass spec is its limited spatial resolution. Nevertheless, with the application of several MS-based techniques in parallel, it is often possible to extract detailed information on the ligand binding modes, intra- and intermolecular conformational changes, and allosteric networks that are critical for enzyme function. As detailed in the description of our other research, the biosynthesis of many natural products and many bacterial virulence mechanisms rely on conformationally dynamic enzymes and protein-protein interactions that remain challenging to study with traditional structural biology. We think that mass spectrometry can make many impactful mechanistic discoveries in these disciplines. In addition to structural biology applications, we also employ mass spectrometry in combination with liquid chromatography to develop novel enzyme activity assays, to perform proteomic and metabolomic studies of bacterial cells, and to develop quantitative assays for other small molecule analytes of interest.

To carry out these studies, our lab operates a Waters Synapt G2-Si Ion Mobility mass spectrometer that can be configured for all of the different measurements we make on a routine basis. Namely, we have an mClass UPLC chromatography system, an autosampler for convenient sample queuing, and an HDX Manager that provides on-line pepsin digestion and LC of deuterium exchanged samples at low temperatures. We have both a standard ESI source as well as a nanospray ESI source for native MS studies of folded proteins and protein-protein/ligand complexes. The mass spectrometer is capable of both collision induced dissociation (CID) and electron transfer dissociation (ETD) modes of ion activation for tandem MS studies, as well as travelling wave ion mobility analysis of the gas phase ions. The ion mobility capabilities are used to characterize the conformational landscape of natively folded protein ions and to increase the peak capacity of HDX-MS workflows. Thus, all of the trainees in our lab will acquire technical skills in mass spectrometry that are highly desirable in the pharmaceutical, agrochemical and biotech industries.