In the last decade, new technologies have emerged to study protein-protein and protein-nucleic acid interactions under near-physiological conditions at large scale. In contrast, development of similar performing technologies for screening and discovery of in vivo metabolite/protein interactions has received little attention. Nonetheless, metabolites comprise a large and important fraction of the cellular molecules. Many can bind proteins as substrates, products, cofactors, and ligands, and thereby constitute metabolic networks or regulate a myriad of environmental and developmental responses, often at very low concentrations. Here, we will establish a performing method for the discovery of novel in vivo protein-metabolite interactions in the model plant Arabidopsis thaliana by adapting an available high throughput protein affinity purification/mass spectrometry platform used for detecting protein-protein interactions. Receptor proteins involved in jasmonate signalling will be used as the model systems to discover new metabolites that interact in vivo with proteins. Ultimately, the role of the identified metabolites and the relevance of their molecular interactions for the jasmonate signalling cascades that steer growth and metabolism will be investigated.