A novel nano- and micro-integrated protein chip (NMIPC) that can detect proteins with ultrahigh sensitivity has been fabricated. A microfluidic network (μFN) was used to construct the protein chips, which allowed facile patterning of proteins and subsequent biomolecular recognition. Aqueous phase-synthesized, water-soluble fluorescent CdTe/CdS core-shell quantum dots (aqQDs), having high quantum yield and high photostability, were used as the signaling probe. Importantly, it was found that aqQDs were compatible with microfluidic format assays, which afforded highly sensitive protein chips for cancer biomarker assays.