Laser ablation mass spectrometry blast through detection in R

Abstract

Rationale: Organisms that grow a hard carbonate shell or skeleton, such as foraminifera, corals or molluscs, incorporate trace elements into their shell during growth that reflect the environmental change and biological activity they experienced during life. These geochemical signals locked within the carbonate are archives used in proxy reconstructions to study past environments and climates, to decipher taxonomy of cryptic species and to resolve evolutionary responses to climatic changes.Methods: Here, we use laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) as a time-resolved acquisition to quantify the elemental composition of carbonate shells and skeletons. We present the LABLASTER (Laser Ablation BLASt Through Endpoint in R) package, which imports a single time-resolved LA-ICP-MS analysis, then detects when the laser has ablated through the carbonate as a function of change in signal over time and outputs key summary statistics. We provide two examples within the package: a fossil planktic foraminifer and a tropical coral skeleton. Results:We present the first R package that automates the selection of desired data during data reduction workflows. This is achieved by automating the detection of when the laser has ablated through a sample using a smoothed time series, followed by removal of off-target data points. The functions are flexible and adjust dynamically to maximise the duration of the desired geochemical target signal, making this package applicable to a wide range of heterogenous bioarchives.Visualisation tools for manual validation are also included. Conclusions: LABLASTER increases transparency and repeatability by algorithmicallyidentifying when the laser has either ablated fully through a sample or across a mineral boundary and is thus no longer documenting a geochemical signal associated with the desired sample. LABLASTER's focus on better data targeting means more accurate extraction of biological and geochemical signals. | INTRODUCTIONLaser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful analytical tool to quantify the elemental composition of a wide variety of natural and anthropogenic materials.A laser beam is focussed to the surface of a target and then pulsed to ablate the sample. Particles from the ablated sample are subsequently transported into an inductively coupled plasma ionisation source then to a mass spectrometer for detection based on the mass-to-charge ratio, which can be converted into a time-resolved isotopic or

Atomic spectrometry update – a review of advances in environmental analysis

“…An R package called LABLASTER was designed 258 primarily to quantify the elemental composition of carbonate shells and skeletons . Data from a single time-resolved LA-ICP-MS analysis were imported into the software package which automatically identified when the laser penetrated the sample or ablated across a mineral boundary.…”