A micro total analysis instrument system is a clinical multiplex instrument intended to measure and sort signals generated by fluorescently-labeled immune complexes from a clinical sample on a microcapillary chip. Signals may be quantified using laser-induced-fluorescence detection using filters on a photodiode or other detector. It may integrate microfluidic chips with discrete zones for clinical sample and assay reagents; capillary electrophoresis; reagent handling system; dedicated instrument control; data acquisition software; raw data storage mechanisms; and other essential hardware components and signal reader unit. It is used with specific assays to comprise an assay test system.