A mobile, self contained molecular diagnostics system is provided with a microfluidic chip, detection apparatus and an integrated or wireless control interface and imager. The system provides automated sample preparation and rapid optical detection of multianalyte nucleic acids and proteins. On chip PCR may be performed to improve the optical fluorescence signal for nucleic acid detections. Plasmonic protein detection is performed using a dark field smartphone microscope. Dark field illumination is based on an evanescent field generated by LED total internal reflection. The smartphone element may also be used as an interface to control the detection apparatus, acquire images, process data and for wireless communications with remote computers. The handheld automated system has low power requirements and is particularly suited for point of care and on demand diagnostics in resource limited settings.