Experimental methods for dissecting the terraincognita of protein-metabolite interactomes

A single metabolite can have diverse biological functions, from biosynthetic intermediates to signaling molecules that binds to one or more proteins. Similarly, a single protein can interact with one or many different metabolites. The extensive and highly dynamic protein-metabolite interaction network affects and shapes all cellular processes. Recent progress in omics technologies has made global profiling of protein-metabolite interaction feasible. Herein, we aim to highlight experimental approaches developed to characterize protein-metabolite interactomes, with particular emphasis on co-fractionation mass spectrometry. We will also discuss remaining grand challenges, including the largely incomplete chemical characterization of metabolomes. •Progress in mass spectrometry is driving novel methods for cell-wide characterization of protein-metabolite interactomes.•Intact protein-metabolite complexes can be separated using classical biochemical approaches.•Recent results attest to previously postulated complexity of the protein-metabolite interactomes.•Dissecting the protein-metabolite interactomes will be essential for a comprehensive functional annotation of metabolomes.