Protocols for rapid identification of small-molecule metabolite ligands interacting with proteins

Metabolite-protein interactions have not been systematically studied due to a lack of effective techniques. Here, we present a protocol for identifying small-molecule metabolite ligands interacting with proteins. We describe steps for mixing the sample with antibodies for immunoprecipitation and applying organic solvent to extract small-molecule metabolites. We then detail procedures for using high-resolution mass spectrometry to quantify small-molecule metabolites bound to proteins. We validate protocol feasibility using the example of an arachidonic acid-Menin protein interaction. For complete details on the use and execution of this protocol, please refer to He et al.¹.