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Date of Award


Document Type

Dissertation - Pacific Access Restricted

Degree Name

Doctor of Philosophy (Ph.D.)



First Advisor

Patrick Jones

First Committee Member

Richard Dodge

Second Committee Member

Paul Gross

Third Committee Member

Larry Spreer

Fourth Committee Member

Richard Turpin

Fifth Committee Member

Robert Mclver


A personal computer based Fourier transform ion cyclotron resonance mass spectrometer has been designed and constructed. An IBM PC AT compatible computer is used to host the interface of the instrument. The advantages of using a personal computer to host the FT-ICR instrument include: (1) very low cost of the computer; (2) extensive graphic and mathematic capabilities; (3) easy performance alteration or expansion; (4) an abundance of application software; and (5) support for a wide range of output devices. A dedicated digital hardware interface, which provides high speed data transfer and accurate timing control, was assembled on the computer's extension board. The extension board is used to replace the frequency synthesizers and waveform recorders normally used for arbitrary waveform generation and data acquisition at a speed of several mega Hertz. The unique features of the digital hardware design include: (1) common memory for both excitation and data acquisition; (2) control logic for critical timing steps; (3) system memory mapping for fast data transfer. This design has not only led to great reduction in construction cost but has increased the flexibility of the instrument to perform complex experiments as well. A general phase modulation algorithm for the stored waveform inverse Fourier transform (SWIFT) excitation has been developed. The method can be used to generate arbitrary excitation waveforms with optimal dynamic range reduction. The maximum entropy spectral analysis (MEM) has been investigated. When the broad-band MEM method was demonstrated in the host computer, resolution and signal-to-noise ratio improvement was observed. New preamplifier, electron beam circuits, and the sample inlet system of the instrument were designed and constructed with computer control. This provides the instrument with reliability, stability, and functionality. A theoretical model for two dimensional Fourier transform ion cyclotron resonance mass spectrometry has been proposed. The model interprets the physical significance of the modulation of the ion signals in the additional dimension. According to the model, the additional time dimension (which is introduced as the duration between the pair of 2D excitation pulses) determines the speed of the primary ions just before the reaction period. The speed modulation may result in primary ion population modulation. In general, the speed modulation will transfer into ion signal modulation through a variety of channels, such as reactions and ion loss. The model also predicts that the ion modulation in the additional dimension is not sinusoidal (therefore, harmonics exist) and the ion signal modulation has definite phase relationships. The implementation of the 2D technique is developed and demonstrated.



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