This papers addresses many of the optimization parameters necessary to convert from high resolution capillary electrophoresis (CE) analytical separation parameters to automated, micropreparative multiple fraction collection using software-controlled, interrupted applied voltage. Optimization of two parameters are crucial: 1) preparative sample loading and 2) the determination of peak collection windows. Factors affecting sample loading volume are discussed, such as capillary inner diameters, sample temperatures and sample injection times. Peak collection windows have been determined experimentally and offer an advantage to windows calculated using a linear mobility relationship, especially for long run times, high current levels, and multiple voltage ramping required for multiple fraction collection. Reinjection analysis of both non-glycopeptides and glycopeptides are examined, and clearly indicate peak mobility can be employed for identifying the collected peptides. Difficulties associated with quantitation of the collected peaks by CE are described and appear to be predominantly associated with sample matrix effects.