Portable mass spectrometers provide convenience for applications where conventional mass spectrometers are not suitable. However, a series of miniaturization issues show up in small mass spectrometers, specifically mass analyzers, that need to be thoroughly addressed before further miniaturization. The work in this dissertation focuses on miniaturization issues of ion trap mass analyzers. Space-charge is one of the major issues in small ion traps affecting their analytical performance. It limits ion trapping capacity when ion-ion repulsion causes spreading of a packet of ions. Simulation studies on the relationship between different trap dimensions and trapping capacity was done on a geometry-optimized cylindrical ion trap. A reasonable way of scaling the two important operating parameters (trapping voltage and trapping frequency as functions of the trap dimension) was discussed and applied in the simulation. The trapping capacity (N) decreased with the physical trap dimension (r0) as expected, and N is scaled exponentially as r0. Scaling laws for trapping parameters are proposed, confirmed by SIMION simulations that evaluate the space charge issue in small ion traps. This effect represents a practical limit in ion trap miniaturization.Geometry deviation is another issue that cannot be neglected in miniaturized ion traps, especially in small linear ion traps (LIT). The LIT our group is working on consists of an assembly of two plates, of which each was made by lithographically patterning a series of electrodes on an insulating plate. It is a promising way of expanding the trap capacity at a small trap dimension. However, misalignment of the two plates might seriously affect its performance, specifically resolution and signal intensity. Simulations were done on the misalignment of two-plate planar LIT in the six possible degrees of freedom (DOF) of misalignment between the two plates. Each DOF's influence on the mass resolution and the ion detection efficiency were discussed. Preliminary data from a previous ceramic plate design was collected while most of the misalignment experiments were done on an improved version. A platform was designed incorporating four motorized stages to precisely control the alignment of the ion trap in vacuum. The new plate design was demonstrated to achieve a better than unit resolution for toluene and deuterated toluene after the plates were aligned. The impact on the resolution and signal intensity from pitch, x-, y- and z-displacement were also experimentally studied.

Mass spectrometry is a technique that analyzes the chemical compositions of compounds based on the mass-to-charge ratio of their ionized constituents. Miniaturized ion trap mass spectrometry finds application in a wide range of fields where portable, rugged, and reliable analytical instruments are required. Ion traps of various designs have been introduced over the past decades, each with their own unique advantages and capabilities. However, the process of developing a novel miniaturized ion trap mass spectrometer continues to be fraught with challenges. This dissertation discusses simulation studies pertaining to the development of a novel dual ion trap, the simplified coaxial ion trap, consisting of a simplified toroidal ion trap and a cylindrical ion trap. Ions are initially trapped in the toroidal region and the target ions are transferred to the cylindrical region where they are fragmented and mass analyzed, while the rest of the ion population remains securely trapped in the toroidal region. The compact design and extended trapping volume secure several advantages that are not available to conventional ion trap designs. The simulations were geared towards the determination of an optimized geometry and optimal operating conditions for the simplified coaxial ion trap. Four main criteria were used in the determination of the ideal geometric and operating conditions; namely, mass-selectivity of transfer from the toroidal to cylindrical traps, transfer and trapping efficiency in the cylindrical ion trap, mass resolution, and unidirectional ejection. The optimized geometry demonstrates successful trapping of ions in the toroidal region and selective transfer of target ions to the cylindrical region. Unidirectional inward ejection of ions could be achieved with a positive hexapole component in the electric field. The mass resolution under optimized conditions of the toroidal trap was 0.3 Da (FWHM), which agrees with the experimental value. The simplified coaxial ion trap yielded a total transfer and trapping efficiency of 25%. A number of suggestions to improve the efficiency are also discussed as part of this work.