The trend towards high throughput applications and miniaturization necessitates approaches capable of microlitre volume sampling and low protein concentration detection. Furthermore, one of the major trends in high throughput screening is the growing replacement of technologies that depend on radioactivity to generate a signal with those that rely on fluorescence. This trend towards non-radioactive detection in general can be understood by some of the advantages inherent to these methods over radioactive modes. These include a significant reduction in safety concerns leading to a relaxation of strict laboratory procedures, elimination of expensive waste disposal, extended shelf-life of labeled reagents, and the possibility of acquiring multiplexed data through the spectral isolation of different wavelength signals. A variety of capillary electrophoretic (CE) approaches utilizing laser-induced fluorescence (LIF) have thus been developed, providing researchers with valuable tools in protein analysis. Various covalent and non-covalent fluorescent derivatization approaches have been investigated, with emphasis on biochemical and/or clinical applications. The non-covalent dye, NanoOrange, is used as a clinical diagnostic tool for early disease diagnosis, quantitating nanomolar concentrations of human serum albumin in solution, and obtaining fluorescence-based biofluid profiles. An alternate non-covalent labeling approach utilizing the fluorescent probe, Sypro Red, and capillary gel electrophoresis allows for rapid, sensitive analysis of protein sample purity as well as molecular weight determination. These two non-covalent approaches are complemented by the development of a fluorescent Insulin-Like Growth Factor-I (IGF-I) analog for use in bioanalytical applications. Specific derivatization reaction conditions were developed to selectively label the N-terminus of the analog hence preserve biological activity. High-performance liquid chromatography and electrospray mass spectrometry were used to confirm the extent of labeling and modification site. Antibody recognition of this fluorescent analog was evaluated using CE-LIF, illustrating the clinical utility of this diagnostic reagent. In addition to the above CE-LIF approaches, a fourth capillary electrophoretic tool is provided for the clinical chemist. Rapid analysis of biofluids is of significant importance in early disease diagnosis. As such, an extensive CE-based analysis of human seminal plasma is presented. Separation conditions, sample stability, and protein/non-protein zone identification issues are addressed. This study and the CE-LIF methodologies discussed above represent original approaches to nanoscale protein analysis.

Capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) is a versatile and sensitive analytical tool with many potential applications. Its advantages over other chromatographic methods include minimal solvent and sample requirements, low waste volumes, simple instrumentation, and diversity of analytes studied. CE is one of the most efficient separation techniques available for the analysis of both large and small molecules, but because few analytes are natively fluorescent, it is necessary to bind them with fluorescent tags if LIF detection is to be employed. These tags increase sensitivity and provide additional separation from components of the sample that do not bind the tags. In this dissertation, four applications of CE-LIF for the determination of tagged analytes are documented. First, a rapid CE-LIF method was developed for the determination of gamma-aminobutyric acid (GABA) and other important brain biogenic amines and amino acids present in biological samples at low levels. The high efficiency and sensitivity necessary to identify toxicologically relevant changes in neurotransmitter levels in brain tissue and microdialysates following Mn exposure was achieved, and the method required minimum sample work-up and quantities of sample for analysis. A linear relationship between the concentration of GABA and the CE-LIF peak height was established, with correlation coefficients of 0.989 or better for four neurotransmitters. Second, the use of two squarylium-based fluorescent dyes (bis-SQHN-4d and SQHN-3c) as noncovalent protein labels was investigated. The fluorescence emissions of both dyes were enhanced upon complexation with model proteins, demonstrating promise as noncovalent fluorescent protein labels. Third, the nature of interactions between two boronic acid-based probes (SQTM-BA1 and ANQW-BA1) and two model proteins (bovine serum albumin (BSA) and hemagglutinin (HA)) have been explored. The complex between SQTM-BA1 and BSA was the only complex to show increased fluorescence emission, and the role of electrostatic interactions between SQTM-BA1 and BSA in complex formation was explored. Lastly, CE-LIF methods were developed to label and quantify turnip yellow mosaic virus (TYMV). Noncovalent labels Red-1c and NN127 effectively labeled the surface proteins of the virus, and the labeled viruses were then analyzed by CE-LIF. The CE-LIF methods developed herein for the analysis of neurotransmitters, free solution proteins, and viruses demonstrate the versatility of the technique, especially when coupled with fluorescent labeling.

Capillary electrophoresis with laser induced fluorescence detection (CE-LIF) is one of the alternative methods being developed for fast and sensitive assays of proteins and peptides. This report summarizes CE-LIF instrument development, efforts at labelling proteins, tests conducted to prove the applicability of CE-LIF to the analysis of samples, and results of a comparison of CE-LIF with some other techniques. Appendices include an instrument operating procedure and a paper that summarizes the experimental details of the protein labelling procedure and a CE-LIF technique for sub-nanomolar assay of proteins.