A novel approach to elucidate the ionization mechanism for the [M + H]+ molecular ion of organic molecules is investigated by molecular depth profiling of isotopically enriched thin films. Using a model bi-layer film of phenylalanine (PHE) and PHE-D8, the results show formation of an [M + D]+ molecular ion for the non-enriched PHE molecule attributed to rearrangements of chemical damage due to successive primary ion impacts. The [M + D]+ ion is observed at the interface for 19.9 nm in the enriched-on-top system and 9.9 nm for the enriched-on-bottom system. This ion formation is direct evidence for dynamically created pre-formed ions as a result of chemical damage rearrangement induced by previous primary ion bombardment events. Copyright © 2012 John Wiley & Sons, Ltd.