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Abstract RationaleThe use of secondary ion mass spectrometry (SIMS) to perform micrometer‐scalein situcarbon isotope (δ¹³C) analyses of shells of marine microfossils called planktic foraminifers holds promise to explore calcification and ecological processes. The potential of this technique, however, cannot be realized without comparison to traditional whole‐shell δ¹³C values measured by gas source mass spectrometry (GSMS). MethodsPaired SIMS and GSMS δ¹³C values measured from final chamber fragments of the same shell of the planktic foraminiferOrbulina universaare compared. The SIMS–GSMS δ¹³C differences (Δ¹³C_SIMS‐GSMS) were determined via paired analysis of hydrogen peroxide‐cleaned fragments of modern cultured specimens and of fossil specimens from deep‐sea sediments that were either untreated, sonicated, and cleaned with hydrogen peroxide or vacuum roasted. After treatment, fragments were analyzed by a CAMECA IMS 1280 SIMS instrument and either a ThermoScientific MAT‐253 or a Fisons Optima isotope ratio mass spectrometer (GSMS). ResultsPaired analyses of cleaned fragments of cultured specimens (n = 7) yield no SIMS–GSMS δ¹³C difference. However, paired analyses of untreated (n = 18) and cleaned (n = 12) fragments of fossil shells yield average Δ¹³C_SIMS‐GSMSvalues of 0.8‰ and 0.6‰ (±0.2‰, 2 SE), respectively, while vacuum roasting of fossil shell fragments (n = 11) removes the SIMS–GSMS δ¹³C difference. ConclusionsThe noted Δ¹³C_SIMS‐GSMSvalues are most likely due to matrix effects causing sample–standard mismatch for SIMS analyses but may also be a combination of other factors such as SIMS measurement of chemically bound water. The volume of material analyzed via SIMS is ~10⁵times smaller than that analyzed by GSMS; hence, the extent to which these Δ¹³C_SIMS‐GSMSvalues represent differences in analyte or instrument factors remains unclear.