Controlled immobilization of peptides onto N-hydroxysuccinimidyl ester functionalized self-assembled monolayer (SAM) surfaces using reactive landing of mass-selected ions has been demonstrated. Surface characterization using time-of-flight secondary ion mass spectrometry and grazing-incidence infrared reflection-absorption spectroscopy confirmed highly efficient covalent linkage through an amide bond formed between the SAM and the free amino group of the lysine side chain. Reactive landing opens a new way for controlled preparation of peptide arrays.