Fourier transform ion cyclotron resonance mass spectrometry instrumentation and methods for structural characterization of trapped biomolecular ions: Innovative MS/MS techniques, gas-phase hydrogen /deuterium exchange, and laser -induced fluorescence

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has become a powerful tool for biomolecular structural characterization because of its superior mass resolving power and high mass accuracy. Of particular interest in this work are the diverse range of fragmentation techniques available to FT-ICR MS/MS, including collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD), and electron detachment dissociation (EDD). Described here is the implementation, development and characterization of FT-ICR based MS/MS techniques for protein and peptide ion dissociation. Also described is the use of gas-phase H/D exchange and fluorescence spectroscopy to probe conformation in gas-phase biological molecules.;Implementation of efficient and rapid collisionally-activated dissociation (CAD) external to an ICR cell (ion threshing) by use of a novel axial electric potential gradient mounted in an external ion accumulation octopole is discussed. Rapid switching of the wire potential between a positive and negative value drives the ion axial motion back and forth and, in the presence of nitrogen gas at suitable pressure, induces dissociation. The method is sufficiently rapid for MS/MS with on-line liquid chromatography (LC) sample introduction. Moreover, compared to CAD in the ICR cell, external CAD improves mass accuracy, producing thermal on-axis fragment ions for detection.;Design and implementation of a permanent on-axis dispenser cathode electron source and off-axis laser geometry that enables simultaneous access to ECD and IRMPD in a 9.4 Tesla FT-ICR mass spectrometer is described. Optimum performance of both fragmentation techniques is maintained.;Infrared and electron irradiation dissociation techniques are primarily applied to structural elucidation of peptides and proteins. The novel application of ECD, EDD, and IRMPD to sulfatides and gangliosides is discussed. These techniques provide extensive structural information for both the ceramide and glycosyl regions of these glycosphingolipids. Also described is the use of mass defect graphical analysis for the simplification of identification of fragment ions. The substantial difference in mass defect between the hydrocarbon and saccharide regions graphically separate into classes.;The development of instrumentation and implementation of electron induced (EIF), and laser induced fluorescence (LIF) and lifetime measurements of mass selected trapped ions is also described. This work includes description of experimental apparatus, implementation of quadrupolar excitation and axialization (QE) for mass selection and ion axialization, as well as results for the EIF, LIF, and lifetime measurements for the trifluorobenzene cation. (Abstract shortened by UMI.).