Data processing for three dimensional mass spectrometry (3D-MS) imaging was investigated, starting with a consideration of the challenges in its practical implementation using a series of sections of a tissue volume. The technical issues related to data reduction, 2D imaging data alignment, 3D visualization, and statistical data analysis were identified. Software solutions for these tasks were developed using functions in MATLAB. Peak detection and peak alignment were applied to reduce the data size, while retaining the mass accuracy. The main morphologic features of tissue sections were extracted using a classification method for data alignment. Data insertion was performed to construct a 3D data set with spectral information that can be used for generating 3D views and for data analysis. The imaging data previously obtained for a mouse brain using desorption electrospray ionization mass spectrometry (DESI-MS) imaging have been used to test and demonstrate the new methodology.

A theoretical method, the harmonic balance method, was introduced to study the coupling effects of hexapole and octopole fields on ion motion in a quadrupole ion trap. Ion motion characteristics, such as ion motion center displacement, ion secular frequency shift, nonlinear resonance curve and buffer gas damping effects, have been studied with the presence of both hexapole and octopole fields. It is found that hexapole fields have bigger impacts on ion motion center displacement, while octopole fields dominate ion secular frequency shift. Furthermore, the nonlinear features originated from hexapole and octopole fields could enhance or cancel each other, which provide us more space in a practical ion trap design process. As an example, an ion trap with improved performance was designed using a specific combination of hexapole and octopole fields. In this ion trap, a hexapole field was used to achieve efficient ion directional ejection, while an octopole field was added to correct the chemical mass shift and resolution degradation introduced by the hexapole field.

A miniature capillary electrophoresis mass spectrometry (CE/MS) system has been developed in this work. A 100% electrical driven miniaturized CE device was integrated with a miniature MS instrument, which has a discontinuous atmospheric pressure interface (DAPI) for coupling with atmospheric pressure ionization sources. A nanoelectrospray ionization (nano-ESI) source was developed with a sheath liquid interface for coupling the miniature CE and the MS system. A systematic characterization and optimization of the analytical performance have been done. The analysis of isobaric peptides and avoiding charge competition effects in nano-ESI sources have been demonstrated.

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