Development of a Fourier transform ion cyclotron resonance/ion mobility spectrometer for structure elucidation of gas phase ions

A novel instrument that combines a Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometer with an ion mobility drift cell was constructed and is demonstrated to yield accurate results. Choice of a FT-ICR mass spectrometer is twofold. First, it allows novel ionic species to be synthesized in the gas phase owing to the trapping nature of FT-ICR mass spectrometry. Second, placing the drift cell within a magnetic field reduces transverse diffusion and increases transmission efficiency through the drift cell because the Lorentz force from the magnet confines the ion's motion in the xy plane. There are significant technological challenges associated with combining FT-ICR and ion mobility, such as differential pumping, aperture alignment, and space limitations that are addressed.; Although ion mobility measurements provide direct information on ion volume-to-charge, explicit structural information is determined by comparing experimental results with theoretical results. Electronic structure methods such as ab initio, semi empirical and molecular mechanics are used to generate low energy conformations, which are then compared with the experimentally observed cross-sections for more detailed structural information.; Electronic structure methods were employed to probe Cu+ binding in peptide ions generated by Matrix-assisted laser desorption ionization (MALDI). Initially basic model systems that simulated amino acid side chains were examined to probe where and how strongly Cu+ was binding (Chapter IV). Excellent correlation between experimental results and these model systems was observed; however, some discrepancies were noticed. A second investigation was initiated to probe whether bidentate Cu+ interactions were the cause of the previously noted discrepancies (Chapter V). Results obtained for bidentate Cu+ interactions with single amino acids are in agreement with experimental results and indicate that bidentate and even multidentate interactions must be considered for metalated gas phase species involving polymeric systems.