While the flexibility of a CO-functionalized tip in scanning probe methods is at the origin of extraordinarily high resolution in imaging, its impact on inelastic electron tunneling spectroscopy has remained unexplored to date. Here, coupled vibrational modes of a CO molecule bonded to the tip of a scanning tunneling microscope and a single melamine isomer on Cu(001) are studied in a combined experimental and theoretical work. Decreasing the distance between CO and the adsorbed isomer causes a s