The measurement of collision cross sections (CCS) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the soft sphere collision model, thus deviating from prior FT-MS CCS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision inducing unfolding and MS/MS experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.
A description of the correction factor used for underestimated CCSs, additional graphs showing the relationships between ion energy, position in the Orbitrap, Orbitrap CCS deviation, and ion m/z, as well as tables of CCS values obtained by IM and Orbitrap CCS measurements are provided.