Determination of Thermochemical Barriers in Multiple-Collision-Induced Dissociation Experiments on Gas-Phase Protein Complexes

In native ion mobility-mass spectrometry (nIM-MS) experiments, biomolecular ions are typically introduced into the gas phase from buffered solution while preserving their native structures, which can then be characterized using gas-phase methods. One of the most important gas-phase characterization techniques available with contemporary commercial mass spectrometers is collision-induced dissociation (CID), in which ions are heated by collisions with neutral buffer gas to cause dissociation, revealing subunit masses and often providing information about quaternary structure. The extent of CID observed is sensitive to instrument design, electric fields, and buffer gas identity and pressure, greatly complicating the comparison of results across instruments and conditions. In contrast, the ion’s underlying potential energy surface is invariant to these conditions and can in principle be probed by accurately modeling ion temperature and dissociation kinetics. Here, the recently developed improved impulsive collision theory, implemented in the “IonSPA” software, is benchmarked against noncovalent dissociation of two prototypical protein complexes, holomyoglobin and Shiga toxin 1 subunit B pentamer, for which thermochemical dissociation barriers were previously reported. Their thermochemical gas-phase unfolding barriers are also determined with IonSPA to provide additional insight into the dissociation process. IonSPA is then used to investigate covalent CID of the well-studied ions ubiquitin and bradykinin, for which significant effects of temperature and initial ion structure are observed compared to previously reported experiments. Despite several simplifying approximations used in IonSPA, these studies illustrate the utility and robustness of IonSPA and pave the way for more quantitative characterization of higher-order native biomolecular structures with gas-phase CID and collision-induced unfolding (CIU).