A static SIMS study was performed using poly(dimethyl siloxane) (PDMS) as a model system to investigate the effects of tertiary structure on the ion formation mechanism and ion formation probability of fragments in the high mass region (> 1000 Da). PDMS produced from anionic polymerization with a narrow polydispersity, can form well-ordered helically coiled monolayers using Langmuir-Blodgett methods at the air water interface, either in a hairpin configuration, if the endgroups are functional or as flat helically coiled chains. Reflection absorption Fourier transform infrared (RA-FTIR) spectroscopic analysis shows the changes in bonding between flat helically coiled PDMS and cast films from dilute solvents, which produces a random coil configuration. Differences between the model systems in infrared spectrum show evidence of changes in structure, producing variation in band formation. Also observed are changes in the band shape and relative peak area between the model systems. These polymeric changes translate into differences in the relative intensities of fragments formed in the repeating pattern of clusters in the high mass ToF-SIMS spectra of the ordered versus the random cast films. Both statistical chain break analysis and molecular mechanics simulations of structure are used to support the analysis. (c) 2006 Elsevier B.V. All rights reserved.