This document discusses the use of nanoparticles encoded with DNA barcodes for ultrasensitive protein detection. It describes a system using magnetic microparticle probes that bind to a target protein via antibodies. Nanoparticle probes encoded with unique DNA barcodes can then sandwich the target. Magnetic separation and DNA dehybridization allows identification of the target protein's barcode, detecting proteins at attomolar concentrations. Multiplexed detection of different protein targets is possible using different barcode sequences on distinct nanoparticle probes.