Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICPMS) is an increasingly popular analytical technique, that is able to provide spatially resolved, minimally destructive analyses of heterogeneous materials. The data produced by this technique are inherently complex, and require extensive processing and subjective expert interpretation to produce useful compositional data. At present, laboratories employ diverse protocols for data processing, and the reporting of these protocols is usually insufficient to allow data processing to be independently replicated, rendering the resulting data untraceable. Importantly, different expert users can obtain significantly different results from the same raw data using nominally identical processing workflows, depending on how ‘contaminants’ are identified and excluded, and which regions of signal are selected as representative of the composition of the sample. The irreproducibility of LA-ICPMS is a significant problem for the technique, but the complexity of the raw data has been a major hindrance to developing traceable data processing workflows. Here, we present LAtools – a free, open-source Python package for LA-ICPMS data processing designed with reproducibility at its core. The software performs basic data processing with similar efficacy to existing software, and brings a number of new data selection algorithms to facilitate reproducible reduction of LA-ICPMS data. We discuss the key advances of LAtools, and compare its output to trace metal analysis of marine CaCO3 (foraminifera) processed both manually and with Iolite, and to manually processed trace element data from zircon grains.

Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales. Understanding the role of templates in biomineral nucleation, and their importance in skeletal geochemistry requires an integrated, multiscale approach, which can place atom-scale observations of organic-mineral interfaces within a broader structural and geochemical context. Here we map the chemistry of an embedded organic template structure within a carbonate skeleton of the foraminifera Orbulina universa using both atom probe tomography (APT), a 3D chemical imaging technique with Ångström-level spatial resolution, and time-of-flight secondary ionization mass spectrometry (ToF-SIMS), a 2D chemical imaging technique with submicron resolution. We quantitatively link these observations, revealing that the organic template in O. universa is uniquely enriched in both Na and Mg, and contributes to intraskeletal chemical heterogeneity. Our APT analyses reveal the cation composition of the organic surface, offering evidence to suggest that cations other than Ca²⁺, previously considered passive spectator ions in biomineral templating, may be important in defining the energetics of carbonate nucleation on organic templates.