A principal difficulty in the structural identification of carbohydrate oligomers by mass spectrometry is the large number of structural isomers that arise from the existence of both different linkage positions between monomer residues and the possibility of multiple linkages to a single residue. Hence, for a straight-chain oligomer, structural identification requires determination of the sequence of glycosyl linkage types, including the linkage positions and the anomeric configurations, as well as the sequence of monomer residues that would be required for characterization of amino or nucleic acid oligomers. Multiple linkages also allow for multiple connection topologies and in biological systems carbohydrates and glycoconjugates commonly exhibit branched as well as linear structures. In the past decades, mass spectral techniques based on ion fragmentation have played a major role in the analysis of carbohydrate structures. In some (select) settings, tandem mass spectrome try is able to provide both a thorough topological characterization and extensive information about glycosidic linkages. In more general settings, information from MS/MS is compromised. The relatively narrow range of atomic species in carbohydrate oligomers leads to isobaric ion fragments. The coexistence of labile glycosidic bonds along with durable pyranose ring structures leads to fragmentation pathways in larger ions that involve almost exclusively the breaking of glycosidic bonds. Ring-opening pathways used in linkage assignments are suppressed. MSn techniques employing ion trap mass spectrometers can address both of these limits. With MSn, ion fragments are also characterized by a generational hierarchy and such characterization can identify structural features. By sequentially dissociating a molecule, ion fragments with a reduced number of degrees of freedom are prepared and their dissociation, in turn, leads to enhanced dissociation of non-glycosidic bonds. The practical potent ial of MSn for carbohydrate analysis hinges on performance aspects of the ion trapping device, i.e., the collision energies that can be obtained and the ion fragment retention in successive generations of ion dissociation. Implementing carbohydrate MSn with FT ICR mass spectrometers is compromised by the analytical need to retain and dissociate relatively small ion fragments with relatively high activation energies. Kinetics of magnetron expansion and ion heating in prototypical carbohydrate MSn experiments are calculated by detailed numerical simulations incorporating both nonlinear-trapping potentials and three-dimensional ion-neutral scattering. In analyzing these experiments, both dynamical instabilities of the ion motion and internal heating are shown to be significant problems. Our main focus of current research in FT-ICR MS is therefore ion dynamics with an emphasis on the problems of implementing remeasurement and MSn. Recent effort has been divided into theoretical/numerical studies of ion dynamics and instrumental modifications associated with implementing cyclotron to axial rotation for the cooling of the ion's translational motion. The numerical objectives are: a) develop bridge code so that electrode potentials generated by a commercial package (SIMION) could be used for trajectory simulation; b) implement stochastic, three dimensional repulsive scattering in the trajectory simulations; c) allow for broadband excitation; d) implement Coulomb coupling between ion pairs; e) output time domain files in a MIDAS compatible format, i.e., have the simulations generate 'spectra'; f) construct a suite of programs to reflect different user objectives and operating environments. The last objective includes developing programs coupled with a graphical user interfa ce (based on CVI LabWindows, National Instruments) to run under Windows 95/NT and shell script controlled programs to run as background processes in a UNIX (Linux) environment. The instrumental modifications for cyclotron to axial rotation have involved the computer design and numerical analysis of various cell and excitation geometries.

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