Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is utilized to investigate the behavior of vapor-deposited K, Au and Ti atoms on several alkanethiol self-assembled monolayers (SAM). The goals are to acquire information about chemical reactions between metal atoms and surface organic functional groups, penetration of metal atoms through the SAMs, growth modes of metal overlayers on top of the SAMs and damage of organic molecules. It is found that appearance of new characteristic peaks and disappearance of initial peaks may indicate chemical reactions or decomposition of organic molecules. The relationship between metal dose and intensity of surface organic functional group-related peaks provides information about penetration or cluster-formation of metal atoms. In addition, removing the metal overlayers by chemical etching and then characterizing samples again is a complementary approach that can reveal valuable information about the location of the metal atoms. (c) 2006 Elsevier B.V. All rights reserved.