G-SIMS is a powerful method for the identification of organics and complex molecules at surfaces. We have previously shown that the molecular structure may be reassembled from fragment ions by studying the evolution of G-SIMS intensities as the surface plasma, with effective temperature T-p, is varied, using a method known as G-SIMS-FPM. Here, we develop a novel approach, based on SMILES (Simplified Molecular Input Line Entry Specification), to assist the reassembly process in an automated way through evaluation of the fragmentation pathways for given molecular structures. A computer program takes a parent structure and goes through every possible fragmentation to provide a tree structure of fragmentation products and simulated fragmentation pathways. For any fragment it is then possible to identify the molecular structure, its mass and a pathway to the parent. We find that there is a good correlation with peak evolution in G-SIMS-FPM data and simulated pathways for two amino acids and a simple peptide. This significantly enhances the application of G-SIMS-FPM to unknown materials. Crown Copyright (c) 2008 Published by Elsevier B.V. All rights reserved.