This report describes a method of controlling the sensitivity and reproducibility of a microchip-based immunoassay by using isotachophoresis to preconcentrate the antigen and antibody prior to binding. Gel electrophoresis separation is coupled to the preconcentration step to separate the immunocomplex products formed. The system employs a quartz-based LabChip that automates the metering, preconcentration, reaction, separation, and detection. The system also uses a handoff mechanism that switches the immunocomplex from the stacking mode to the separation mode. We show that the handoff timing affects the data quality and repeatability of the electropherograms, and we demonstrate an automatic handoff mechanism to precisely control the signal intensity and separation of peaks of interest. In so doing, the automatic handoff mechanism also improves the reproducibility of the assay. When applied to the homogeneous liquid-phase detection of alpha-fetoprotein, a common tumor marker, the system shows a greater than 200-fold stacking of specific analytes of interest.