The amount of internal energy imparted to the ions prior to the ion mobility cell influences the ion structure and thus the collision cross section. Non-covalent complexes with few internal degrees of freedom and/or high charge densities are particularly sensitive to collisional activation. Here, we investigated the effects of virtually all tuning parameters of the Agilent 6560 IM-Q-TOF on the arrival time distributions of ubiquitin7+ and found conditions in which the native state prevails. We discuss the effects of solvent evaporation conditions in the source, of the entire pre-IM DC voltage gradient, of the funnel RF amplitudes. We also report on ubiquitin7+ conformations in different solvents, including native supercharging conditions. Collision-induced unfolding (CIU) can be conveniently provoked either behind the source capillary or in the trapping funnel. The softness of the instrumental conditions behind the mobility cell was further optimized with the DNA G-quadruplex [(dG4T4G4)2·(NH4+)3-8H]5-, for which ion activation results in ammonia loss. To reduce the ion internal energy and obtain the intact 3-NH4+ complex, we reduce the post-IM voltage gradient, but this results in a lower IM resolving power due to increased diffusion behind the drift tube. The article describes the various trade-offs between ion activation, ion transmission, and ion mobility performance for native MS of very fragile structures. Graphical Abstract ᅟ.
Keywords: Ion activation; Ion mobility; Native MS; Nucleic acids; Proteins.