The size-dependent interactions of eight blood proteins with silver nanoparticles (AgNPs) in their binary mixtures were investigated using surface-enhanced Raman scattering (SERS). Principal component analysis (PCA) was performed on the SERS spectra of each binary mixture, and the differentiation ability of the mixtures was tested. It was found that the effect of relative concentration change on the SERS spectra of the binary mixtures of small proteins could be detected using PCA. However, this change was not observed with the binary mixtures of large proteins. This study demonstrated that the relative interactions of the smaller proteins with an average size of 50 nm AgNPs smaller than the large proteins could be monitored, and this information can be used for the detection of proteins in protein mixtures.