The understanding of the physicochemical properties of proteins in solution is required to understand the separations taking place in the capillary. For example, during isoelectric focusing, it is important to ensure the lack of protein precipitation during fOCUSing and mobilization otherwise artifacts occur and the true resolution of charge variants is not achieved. Similarly, buffer conditions, including additives, composition of buffer, and pH can influence the resolution of product variants. With diligent efforts one can achieve desired separations. As knowledge of buffer conditions and use of these techniques increase, the methods will be improved.MECC can be useful for the characterization of recombinant proteins and monoclonal antibodies. However, the relatively long analyte migration times may be a deterrent for routine use in quality control situations. Pharmaceutical companies will employ new techniques which provide advantages over current technology. CE has advantages in certain applications. Applications which use slab gel techniques, IEF and SDS-PAGE can be replaced by the CE methods for formulation development, characterization of charge isoforms, and for purity determinations. CZE and clEF can be used for rapid identity tests which do not require peptide mapping. CZE has a tremendous advantage in analyzing basic proteins, and CZE and CE-SDS can be used to quantify product in the presence of interfering excipients. It is the responsibility of the analytical chemist to determine applications which are appropriate for CEo It is apparent that these are currently being defined for the biotechnology industry, and the usage of CE should continue to increase.