A pneumatic method, and associated apparatus, for injecting a discrete sample plug into the separation channel of an electrophoresis microchip (100) is disclosed. In a first step, pressurized gas (90) is applied to the sample (30) and background electrolyte (20) reservoirs such that the pressure is higher there than at the sample waste reservoir (35) to create a focused sample stream at the junction between the sample and separation channels. In a second step, the pressure at the sample reservoir (30) is reduced in order to pneumatically inject the sample plug into the separation channel. The waste reservoir (35) may be connected to a pressure reducing device (91). The methods, systems and devices are particularly suitable for use with a mass spectrometer (200i).