Electrokinetic supercharging has been integrated in CZE for the development of a highly sensitive methodology for protein tryptic digest analysis. A careful choice of the experimental conditions led to sensitivity enhancement factors between 1000 and 10,000 whilst maintaining a satisfactory resolution. Peptides in the low nanomolar concentration range have been detected despite the use of the poorly sensitive UV absorbance detection mode. The buffer system used in this study is fully suitable for coupling CE to MS.