An automated multiplex detector system includes: (a) a nucleic acid amplification compartment for amplifying nucleic acid of one or more targets in a sample, and (b) an analysis compartment in fluid communication with the amplification compartment, the analysis compartment housing a nanoparticle-based multiplex detector capable of using the amplified nucleic acid of the amplification compartment and producing a signal that correlates with the presence of the one or more targets in the sample.