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
