Optimizing Native Ion Mobility Q-TOF in Helium and Nitrogen for Very Fragile Noncovalent Interactions

TL;DR

This study systematically optimizes ion mobility Q-TOF parameters in helium and nitrogen to preserve fragile noncovalent structures, enabling more accurate CCS measurements and structural analysis.

Contribution

It provides a comprehensive analysis of tuning parameters affecting native ion mobility measurements and proposes optimized conditions for fragile noncovalent complexes.

Findings

Optimized source and funnel conditions preserve native ubiquitin conformations.

Reduced post-IM voltage gradient decreases internal energy but lowers IM resolution.

Trade-offs identified between ion activation, transmission, and mobility resolution.

Abstract

The meaningful comparison of ion mobility (IM) results and of collision cross section (CCS) values on different platforms is a prerequisite for using CCS for identification or structural assignment. The amount of internal energy imparted to the ions prior to the ion mobility cell is a source of experimental variation. 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 will discuss the effects of solvent evaporation conditions in the source, in the entire pre-IM DC voltage gradient, and with the funnel RF amplitudes, and will also report on ubiquitin7+ conformations in different solvents, including native supercharging conditions. Collision-induced unfolding (CIU) can be conveniently provoked in two distinct regions: behind the source capillary (by changing the fragmentor voltage) and in the trapping funnel (by changing the trap entrance grid delta voltage). The softness of the instrumental conditions were then optimized with the benchmark 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 reduced the post-IM voltage gradient, but this resulted in a lower IM resolving power due to increased diffusion behind the drift tube. The article thus describes the various trade-offs between ion activation, ion transmission, and ion mobility performance for native MS of very fragile structures.