15 keV Ga+ ion impact and the thermal decomposition of arginine molecules has been simulated by quantum molecular dynamics (QMD). We obtained the calculated mass spectra which express the distribution for fragment molecule generated by ion impact or thermal decomposition. From the comparison between the experimental TOF-SIMS spectra and the calculated spectra, we discussed the fragmentation mechanism of arginine molecule by Ga+ ion impact. (C) 2008 Elsevier B. V. All rights reserved.