Methods for analyzing reaction products from an assay chamber (11) in a microfluidic device comprise the steps of (I) moving a sample from the chamber (11) into a load channel (12), towards a separation channel (4), and (III) analyzing the sample present at an intersection (16) of the load channel (12) and the separation channel (4), by electrophoretic separation in the separation channel (4). During this separation, the step of (II) moving a next sample inside the load channel, towards a preload channel (13), is carried out.