MALDI-TOF MS-based peak differences in oxacillin-resistant Staphylococcus aureus and oxacillin-susceptible S. aureus isolates have been described previously. Unfortunately, these isolates were not isogenic with respect to their mecA gene. Ours is the first to use a SCCmec-harboring parent and a SCCmec-lacking daughter strain, with the same genetic background, to unequivocally rule out strain-specific protein peaks. We could not show differences in the peak profiles within the preset Biotyper settings used for MALDI-TOF-based identification in this pair of SCCmec-harboring parent and SCCmec-lacking daughter strains.