Abstract: A method is provided for determining the presence of multiple different target analytes in a liquid sample using electrophoretic separation and magnetic labels within a self-contained reaction cartridge and an external magnetic sensor for detection. Magnetic labels are bound to target analytes through specific binding elements. By electrophoretic separation, the multiple different targets can be sorted according to their specific sizes and inherent molecular charges for better detection resolution and specificity. After the separation process, the target analytes are then recognized and trapped by the detection binding elements within the reaction cartridge. A magnetic field generator provides a changeable magnetic field that causes the bounded magnetic labels and target analytes to produce a resonance disruption detectable by a magnetic sensor. The sensor can provide a digital binary value to indicate whether or not a label particle is bound and that determines the presence of target analytes.