A series of Methionine (Met) derivatives, where either the amino group and/or the carboxylic acid group is blocked by acetyl and/or methyl ester functionalities, has been investigated by Collision Induced Dissociation‐tandem mass spectrometry (CID‐MS2) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. The CID‐MS2 experiments were performed using a Fourier‐transform ion‐cyclotron‐resonance (FT‐ICR) mass spectrometer equipped with an electrospray ionization (ESI) source. The IRMPD spectra were recorded employing a Paul type ion‐trap coupled with the free‐electron laser (FEL) FELIX in the fingerprint region from 600 to 2000 cm‐1. We show that the oxidation of the methionine residue with protected terminal groups induces the formation of a sulfoxide group. However, compared to the IRMPD spectrum of protonated methionine and methionine sulfoxide, significant spectral differences are observed in the spectra of model peptide backbones containing methionine. DFT calculations show that protonation occurs on the sulfoxide group in the gas phase for these model peptide backbones containing methionine, shifting the diagnostic signature of the sulfoxide group from 1000 to 862 cm‐1.