This learning module is written for undergraduate chemistry researchers who are already familiar with fundamentals and basic aspects of capillary electrophoresis system such as those outlined in Learning Module I. The experiment outlined in this Module may be accomplished using a commercial or custom-built capillary electrophoresis instrument. The first 8 steps of this learning module explore sample introduction for capillary electrophoresis. Steps 9 and 10 require the user to formulate protocol for quantitative and qualitative analysis by capillary electrophoresis. The last step (11) requires an assistant or colleague to prepare a sample of unknown concentration that will be used for a practical laboratory experiment. This exercise will allow the user to assess her or his laboratory skill and knowledge of the operation of a capillary electrophoresis instrument. The experiment outlined here is performed with recommended chemicals (atenolol, mesityl oxide, naproxen). The experiment may be completed with other compounds, and alternative chemicals are outlined in the instructor’s manual accompanying this material. Successful completion of Learning Module II requires you perform runs under various injection conditions and draw conclusions regarding the optimal injection protocol; (2) document standard protocol for quantitative and qualitative analysis; and (3) assess your proficiency at qualitative and quantitative analyses.