Development of Ion Mobility Mass Spectrometry Instrumentation to Investigate the Gas-Phase Structures of Protein and Protein Complex Ions

Abstract

This dissertation reports the development of new ion mobility mass spectrometry (IM-MS) instrumentation to analyze protein and protein complex ions. IM-MS is a gas-phase analytical technique that separate ions based on their collision cross section (a description of ion shape) and mass-to-charge ratio. Electrospray ionization of samples from buffered solutions at biologically relevant pH generates “native-like” protein ions, which retain noncovalent interactions and compact conformations. IM-MS analysis enables the determination of the shape and assembly of native-like ions, which can be used to infer information about the solution conformations of biomolecules. New IM devices were developed to improve the informational content obtained from IM-MS experiments. First, an RF-confining drift cell was developed and implemented in a commercial mass spectrometer. Experimental results and ion trajectories implemented using SIMION were used to describe the separation principles of ions in RF-confining drift cells. Those results show that RF-confining drift cells separate ions similarly to traditional IM devices and that applied RF potentials have minimal effects on the effective temperatures of gas-phase ions. The RF-confining drift cells was used to report collision cross sections for 349 ions, 155 of which are for ions that have not been characterized previously using IM. The effects of ionization conditions and analyte solutions on the charge states and collision cross sections of ions was also investigated. An additional IM device based on Structures for Lossless Ion Manipulations (SLIM) was developed. SLIM is an emerging IM technology that can be implemented as modular platforms to perform ion separations, filtering, and trapping. The first collision cross sections determined using SLIM are reported. IM analysis of native-like protein ions shows that those ions exhibit significant structural heterogeneity in the gas-phase. To evaluate the stability and dynamics of native-like protein ions, IM-IM-MS functionality was implemented into the SLIM device. Dynamic gas-phase conformations were observed for native-like protein ions, which has significant implications for the broader community’s interpretation of IM-MS results. The stability of structural subpopulations of native-like ions was investigated as a function of gas-phase ion lifetime at near-ambient temperatures. The conformations of subpopulations evolve continuously in the gas-phase, but even after 4 seconds, the subpopulations exhibit different distributions of collision cross sections. This suggests that native-like ions in IM-MS experiments can retain some memory of their initial gas-phase structures for up to seconds at near-ambient temperature.