This paper describes an application of attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and surface-enhanced infrared spectroscopy (SEIRA) to characterize the selective adsorption of four peptides present in body fluids such as neuromedin B (NMB), bombesin (BN), neurotensin (NT), and bradykinin (BK), which are known as markers for various human carcinomas. To perform a reliable analysis of the SERIA spectra of these peptides, curve fitting of these spectra in the spectral region above 1500 cm-1 and SEIRA measurements of sulfur-containing and aromatic amino acids were performed. On the basis of the analyses of the spectral profiles, specific conclusions were drawn regarding specific molecule-metal interactions and changes in the interaction during the substrate change from the surface of silver nanoparticles (AgNPs) to gold nanoparticles (AuNPs).