The goal of this project is to study capillary electrophoresis (CE) and electroosmotic flow (EOF) and the variations in EOF that decrease the reproducibility of CE. This study focuses on the reproducibility problems of EOF. Electroosmotic flow is affected by changes in temperature; pH, viscosity, ionic strength and molecular adsorption to the surface of the capillary. The net velocity of an analyte molecule in CE is ν_net = ν_{electrophoresis} + ν_{electroosmosis}, and variations in EOF will lead to variations in migration times for analyte peaks. We use measurements of EOF vs. time to correct electropherograms to improve reproducibility. This method is then compared to published correction methods using one neutral marker and multiple electrophoretic markers to determine which method performs best.

To measure EOF, a photobleaching technique is used. Electroosmotic flow is measured by determining the time required for a photobleached zone of a neutral fluorescent dye to travel through the capillary from a starting point at the bleaching beam focal point (F1) to a position at the fluorescence detection beam focal point (F2) over a set distance. To generate the photobleached zone a shutter is opened for a brief period of time exposing the neutral fluorescent dye in the capillary to the bleaching beam. After the shutter closes, the zone travels from F1 to F2. The flow rate is then simply measured as flow rate= d_F1-F2/Δt_F1-F2. This technique produces a record of EOF versus time, which allows us to correct data to account for EOF fluctuations during a separation.