Atomic depth profiling using secondary ion mass spectrometry, SIMS, is common in the field micro-electronics; however, the generation of molecular information as a function of sample depth is difficult due to the accumulation of damage both on and beneath the sample surface. The introduction of polyatomic ion beams such as SF5 and C-60 have raised the possibility of overcoming this problem as they deposit the majority of their energy in the upper surface of the sample resulting in increased sputter yields but with a complimentary reduction in sub-surface damage accumulation. In this paper we report the depth profile analysis of the bio-polymer polycaprolactone, PCL, using the polyatomic ions Au-3(+) and C-60(+) and the monoatomic Au+. Results are compared to recent analysis of a similar sample using SF5+. C-60(+) depth profiling of cellulose is also demonstrated, an experiment that has been reported as unsuccessful when attempted with SF5+ implications for biological analysis are discussed. (c) 2006 Published by Elsevier B.V.