Grazing incidence infrared reflection absorption spectroscopy (IRRAS) for in situ and in real time characterization of substrates modified by soft and reactive landing (SL and RL) of complex ions was implemented on a massselected ion deposition instrument. Ions produced by electrospray ionization were mass-selected using a quadrupole mass filter and deposited onto inert and reactive self-assembled monolayer (SAM) surfaces. Surface composition during and after ion deposition was monitored using IRRAS. Physisorption of a cyclic peptide, Gramicidin S (GS), was studied for 8 h during deposition and additional 12 h after the end of deposition. The integrated signal of the characteristic amide bands followed a linear increase during the deposition and stayed unchanged after the deposition was finished. Similar linear increase in IRRAS signal was obtained following reactive deposition of the protonated dodecanediamine onto SAMs of dithiobis (succinimidyl undecanoate) (NHS-SAM) and 16-mercaptohexadecanoic acid fluoride (COF-SAM) on gold. IRRAS allowed us to monitor for the first time the formation of the amide bond between reactive SAM surfaces and the projectile molecule.