A portable and completely self-contained apparatus(20) for detecting analyte and the methods of use thereof is described. The apparatus (20) includes a microfluidic cartridge driver unit (30), an optical inspection unit (32), and a control unit (28) and a power supply unit, which can run the binding and detection of the analyte without any fluidic interfaces to the instrument. The microfluidic cartridge driver unit (30) receives microfluidic cartridge (22) that holds a microarray and integrated microfluidic chip (24) for delivering the analyte to perform different process steps in the detection of analyte. A complete detection of analyte using the invention takes only a few minutes.