Characterization of rectilinear ion traps and extension of an ion trajectory simulation program to electrode configurations with arbitrary geometries

The objective of the thesis is to fully apply a computational simulation tool, the program Ion Trajectory SIMulation program ITSIM, to elucidate the complex ion motion inside a mass spectrometer system, so facilitating instrumentation development and guiding designs for new experiments. This required the extension of the capabilities of the program and experiments on a variety of ion trap instruments. A mass analyzer based on a rectilinear geometry ion trap (RIT) has been built and its performance has been characterized. Design concepts for RITs are delineated with emphasis on the effects of electrode geometry on the calculated electric field and an appropriate distribution of higher-order electric field contributions allows selection of an optimized geometry. The demonstrated capabilities of the RIT include large ion trapping capacity, tandem mass spectrometry, a mass resolution in excess of 1000, and a mass/charge range of 650 Th. An optimization procedure has been developed for the cylindrical ion trap (CIT) based on field calculations and simulations of ion motion. The geometrical effects were systematically investigated and optimized. Appropriate compensation by introducing high-order field components, namely octapolar and dodecapolar fields, was used to refine the CIT geometry and so to improve mass resolution in mass scans using boundary and resonance ejection. Design considerations for the miniature ion trap are also discussed in detail in terms of pseudopotential well depth, trapping efficiency, pressure and space charge effects. An improved multi-particle ion trajectory simulation program, ITSIM 6.0, is described which is capable of ion trajectory simulations for electrode configurations with arbitrary geometries. The electrode structures are input from a 3D drawing program AutoCAD and the electric field is calculated using a 3D field solver and ITSIM 6.0. It converts the calculated electric field into a field array file readable by ITSIM 6.0 and ion trajectories are calculated by solving Newton\u27s equation using Runge-Kutta methods. Simulations of ion motion in a variety of 3D devices, e.g. ion transport systems and linear ion traps, demonstrate both the qualitative and quantitative characteristics of ITSIM 6.0