The enhancement of weak Raman signals has been challenged to obtain high-quality signals of surface-enhanced Raman scattering (SERS). By employing the Parkinson's disease-related protein of α-synuclein, we introduce SERS-active gold nanoparticles (AuNPs) individually isolated with an ultrathin α-synuclein shell and their 2-D array into a tightly packed monolayer on a glass support, which permits a quantitative SERS measurement of phthalocyanine tetrasulfonate (PcTS), a chemical ligand of the pathological protein. Subsequently, the PcTS-bound SERS substrate was also shown to be capable of discriminating two biologically important metal ions of iron and copper by detecting copper ion to the sub-ppm level in a highly selective manner via the in situ chemical reaction of metal chelation to PcTS. The strategy of using the protein-based 2-D AuNP SERS platform, therefore, could be further developed into a custom-made protein-based biosensor system for the detection of not only specific chemical/biological ligands of the immobilized coat proteins but also their biochemical reactivities.