One of the main area of our research, supported by the MIRA grant R35 GM118078, entitled Analysis and Prediction of Molecular Interactions, is investigating the interactions between proteins and small molecules, including drugs and metabolites. Bioactive small molecules, such as the products of cellular metabolism, natural products and synthetic organic compounds, are potent mediators of biological processes as ligands and allosteric regulators. Mapping their physical associations is therefore a critical but challenging task. To this end, we seek NIGMS administrative supplements to acquire a high performance Thermo Scientific Q-Exactive Plus Orbitrap Mass Spectrometer (QE+MS) to support our efforts to explore and exploit the dynamic interactions of small molecules with cellular proteins, biochemical pathways and signaling cascades. We plan to use this instrument together with our new colleague and collaborator, Andrew Emili, a recent recruit to Boston University and leader in using mass spectrometry to map protein interaction networks, to study protein-metabolite interactions (PMIs) in a rigorous experimental manner. Our computational modeling predicts many novel interactions that require stringent experimental validation, which currently stretches the limited MS capabilities available to us. In addition to providing valuable information on potential PMIs, mass spectrometry will address a major challenge in differentiating putative functional regulatory interactions from non-specific interactions that do not entail functionality. This problem is an excellent fit for the structural modeling methods developed in our lab, and we will thus work in a synergistic, iterative manner to apply computational tools to analyze and prioritize experimental interaction data provided by the proposed mass spectrometry instrumentation for the identification of PMIs that are most likely functional. Although establishing functionality will still require other biological tests (e.g. enzyme assays), we expect to develop systematic methods that reduce the number of compounds that need to be investigated in such a demanding, low throughput manner. Having access to a state-of-the-art protein-metabolite interaction platform and our collaborations with Dr. Emili will be very productive and lead to fruitful new avenues for our research program. The collaboration will also engage us with the team of Dr. Daniel Segre at Boston University, whose lab studies complex metabolic networks, and thus will directly contribute to the identification of novel protein-metabolite interactions. Dr. Segre’s research is supported by the grant R01GM121950 “A platform for mining, visualization and design of microbial interaction networks”, and he is also requesting an administrative supplement to support the acquisition of the proposed mass spectrometer. The University’s commitment is demonstrated by its investment in renovating the infrastructure for supporting this multi-user research instrument and by the Department of Biology’s provision of partial support for an ongoing service contract to ensure its operation.