Nondenaturing Mass Spectrometry to Study Noncovalent Protein/Protein and Protein/Ligand Complexes: Technical Aspects and Application to the Determination of Binding Stoichiometries

In the present chapter we detail how mass spectrometry (MS) can be used to characterize noncovalent complexes, especially multimeric proteins and protein/ligand complexes. This original application of MS, also called “supramolecular MS” or “nondenaturing MS,” appeared in the early 1990s and has continuously evolved since then. Nondenaturing MS is now fully integrated in structural biology programs and in drug discovery platforms. Indeed, appropriate sample preparation and fine tuning of the instrument make it possible to transfer weak assemblieswithout disruption fromsolution into the gas phase of themass spectrometer. In this chapterwe detail experimental conditions (sample preparation, optimization of instrumental parameters, etc.) required for the detection of noncovalent complexes by MS. We then focus on the type of information and accuracy that we get after interpreting electrospray ionization mass spectra obtained under nondenaturing conditions, with emphasis on the determination of the stoichiometry of protein/protein and protein/ligand complexes.