Abstract: Nanoparticle composites and method of use thereof for simultaneously sensing and probing a biological system, comprising providing a nanoparticle composite comprising a nanoparticle comprising a core and a shell; a first ligand bound to the nanoparticle, said first ligand capable of sensing pH; a second ligand bound to the nanoparticle, said second ligand distinct from said first ligand and capable of binding to a target; and bringing the nanoparticle composite into contact with the biological system to produce a first and a second pH-dependent signal; and analyzing the first or the second signal by means of surface-enhanced Raman spectroscopy.