Aspects of the innovations presented herein relate to improved systems that in some embodiments perform capillary electrophoresis (CE) and CE in conjunction with electrospray ionization (ESI) as an input to a mass spectrometry system (MS). Some embodiments use a high voltage isolated CE power supply that is configured to float on the high voltage output of an ESI-MS power supply, with a protective resistance in the ESI-MS path, as well as DC/DC converter isolation and communication system isolation for the isolated CE power supply. Some embodiments additionally use a cartridge assembly integrating separation and conductive fluid capillaries with fluid cooling and protective retractable housings for the capillary end portions and for the ESI output. The protective housing may further be used with an adapter for interfacing with different MS systems.