Interaction between metabolites and proteins drives virtually all cellular regulatory processes within any organism as well as the interaction between different organisms. Recent reports highlight that numerous plant metabolites embrace multiple biological activities, beyond a sole role as substrates, products or co-factors of enzymes, or as defense or growth regulatory compounds. Though several technologies have been developed to identify and characterize metabolite-protein interactions, the effective and systematic implementation of such methods in the plant field remains limited. Therefore, we have installed a Limited Proteolysis Mass spectrometry (LiP-MS) platform for the mapping and identification of protein-metabolite interactions (from plants or other organisms). We extensively use this platform to reveal hitherto unknown targets of plant metabolites with a signaling function, bioactive defense metabolites and xenobiotics. Thereby, we aspire to increase our fundamental understanding of plant metabolite-dependent regulatory networks and, eventually, also to empower agrochemical and drug discoveries.