Through analyzing mixtures of compounds of known gas-phase basicities, the importance of this property on the secondary ions emitted from a surface under primary ion bombardment is investigated. The aim is to obtain a greater understanding of the ionization mechanisms that occur in secondary ion mass spectrometry (SIMS). The commonly used matrix assisted laser desorption/ionization (MALDI) matrix 2,4,6-trihydroxyacetophenone (THAP) and a range of low molecular weight biomolecules were used to investigate whether analyte/matrix suppression effects that have been observed in analogous MALDI experiments were also present in static-SIMS. The outcome of the experiments demonstrates that strong suppression of the quasi-molecular signal of one molecule in a mixture can occur due to the presence of the other, with the gas-phase basicity of the compounds being a good indicator of the secondary ions detected. It is also demonstrated that the suppression of the quasi-molecular ion signal of a compound in a two-component mixture can be minimized by the inclusion of a third compound of suitable gas-phase basicity. (J Am Soc Mass Spectrom 2007, 18, 1559 -1567

Although the benefits of decreased sample temperature for the molecular profiling of organic materials with time-of-flight secondary ion mass spectrometry (TOF-SIMS) have been established, the mechanism behind spectral changes observed at low temperature, particularly increased protonated molecular ion (M + H)(+) yields, have not been examined in detail. We have developed a procedure to investigate these effects by monitoring secondary ion yields under sustained primary ion bombardment as the sample temperature is cooled from room temperature down to 80 K. Examination of biomaterials such as an amino acid (arginine), a polypeptide (Gly-Gly-Tyr-Arg), a lipid (1,2 dipalmitoyl-sn-glycero-3 phosphatidylcholine), and a drug molecule (cyclosporine A) each provide evidence of ion yield enhancement at 80 K under either 20 keV C(60)(+) or 20 keV Au(3)(+) bombardment. For example, arginine shows a 2-fold increase in the steady-state intensity for the (M + H)(+) ion at 80 K compared to the steady state at 300 K. It is shown that there is a correlation between the yield enhancement and a reduction in the damage cross section, which for arginine under 20 keV Au(3)(+) bombardment decreases from 5.0 ± 0.4 × 10(-14) cm(2) at 300 K to 2.0 ± 0.3 × 10(-14) cm(2) at 80 K. The role of water as the facilitator for this reduction is explored through the use of H(2)O and D(2)O dosing experiments at 80 K.

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