FlexMAP 3D bead-based multiplexing assay system simultaneously measures up to 500 analytes in a single microplate well. This multiplexing ability enables broadening the types of testing performed using bead-based multiplexing. The system also offers a high-throughput module and the ability to interface with liquid handlers. Instrument features include digital technology, redesigned optics, a dual syringe assembly, an auto-adjusting probe and software to enable automation, and the ability to use both 96 and 384 well plates.