An integral probe for capillary zone electrophoresis/continuous-flow fast atom bombardment mass spectrometry was constructed and operated in either the coaxial or liquid-junction interface mode. Results using these interfaces for the analyses of synthetic peptides are presented. The coaxial arrangement attains the best electrophoretic performance, generally providing a greater number of theoretical plates. However, in that the electrophoresis times are generally greater for the liquid-junction interface because there is no mechanical flow resulting from the source vacuum, the overall separation efficiency of the liquid-junction interface is equal to or greater than that of the coaxial interface. In addition, the liquid-junction interface is easier to set up and operate, and allows larger inner diameter capillaries to be used to achieve higher sample loads.