In this technique, the goal is to preserve a biomolecule – most often a protein or complex – in a state that is as close as possible to how it is folded in its native environment before transferring it into the gas phase for analysis by MS. This approach can reveal important insights into complex stoichiometry and (dis)assembly pathways, including the equilibrium between different states.

Going further, it is possible to use gas-phase fragmentation of native noncovalent complexes to either eject subunits or even induce cleavage of covalent bonds to identify the subunits. Excitingly, the preference for certain fragmentation sites in these experiments often contains information about the 3D structure of the complex. This is a relatively new field which we, in collaboration with labs from around the world, are pushing beyond the current state-of-the-art.

Native MS is a powerful technique for studying the stoichiometry of complexes, but it is not trivial to tell whether a protein is folded or unfolded, especially if it is part of a larger complex or if several (partially) folded states co-exist. Ion mobility spectrometry directly measures the physical size of an ion in the gas phase and can therefore provide this missing information. In combination with (native) mass spectrometry, subunit identity, stoichiometry, and folding state can all be investigated using a single instrument.

Here, a protein is dissolved in deuterium oxide (heavy water), resulting in exchange of amide hydrogens for deuterium. This leads to a mass shift, which is easily detectable with mass spectrometry. The rate of deuterium uptake depends on surface accessibility and local backbone flexibility. This approach therefore is excellent for probing binding surfaces and secondary protein structure, and provides complementary information to the methods described above.