The invention provides a capillary isoelectric focusing (cIEF) system based on a sandwich injection method for automated chemical mobilization. This system was coupled with an electrokinetically pumped nanoelectrospray interface to a mass spectrometer. The nanoelectrospray emitter employed an acidic sheath electrolyte. To realize automated focusing and mobilization, a plug of ammonium hydroxide was first injected into the capillary, followed by a section of mixed sample and ampholyte. As focusing progressed, the NH3H2O section was titrated to lower pH buffer by the acidic sheath buffer. Chemical mobilization started automatically once the ammonium hydroxide was consumed by the acidic sheath flow electrolyte.