A miniature capillary electrophoresis mass spectrometry (CE/MS) system has been developed in this work. A 100% electrical driven miniaturized CE device was integrated with a miniature MS instrument, which has a discontinuous atmospheric pressure interface (DAPI) for coupling with atmospheric pressure ionization sources. A nanoelectrospray ionization (nano-ESI) source was developed with a sheath liquid interface for coupling the miniature CE and the MS system. A systematic characterization and optimization of the analytical performance have been done. The analysis of isobaric peptides and avoiding charge competition effects in nano-ESI sources have been demonstrated.