G-SIMS is an easy to use method that considerably simplifies complex static SIMS spectra. The G-SIMS peaks relate directly to the parent molecular structure and so provide a library independent method for direct interpretation and identification. For larger molecules (> 100 u) the mass alone may be insufficient to identify the molecule unambiguously. A development of G-SIMS, G-SIMS-fragmentation pathway mapping (FPM), solves this problem. G-SIMS-FPM allows the molecular structure to be re-assembled by following fragmentation pathways as the G-SIMS surface plasma temperature is varied. In this study, we develop the inclusion of negative secondary ion fragmentation data to provide a more complete analysis. This approach is exampled with data for complex molecules of Irganox 1010 and folic acid. Crown Copyright (c) 2006 Published by Elsevier B.V. All rights reserved.