Laser ablation mass spectrometry blast through detection in R
Laser ablation mass spectrometry blast through detection in R
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 algorithmically identifying 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.
e9533
Searle-Barnes, Alex
27cd9e5f-9a76-4d3d-8c88-0d3d0b1fad63
Milton, James A.
9e183221-d0d4-4ddb-aeba-0fdde9d31230
Standish, Christopher D.
0b996271-da5d-4c4f-9e05-a2ec90e8561d
Foster, Gavin L.
fbaa7255-7267-4443-a55e-e2a791213022
Ezard, Thomas H. G.
a143a893-07d0-4673-a2dd-cea2cd7e1374
15 August 2023
Searle-Barnes, Alex
27cd9e5f-9a76-4d3d-8c88-0d3d0b1fad63
Milton, James A.
9e183221-d0d4-4ddb-aeba-0fdde9d31230
Standish, Christopher D.
0b996271-da5d-4c4f-9e05-a2ec90e8561d
Foster, Gavin L.
fbaa7255-7267-4443-a55e-e2a791213022
Ezard, Thomas H. G.
a143a893-07d0-4673-a2dd-cea2cd7e1374
Searle-Barnes, Alex, Milton, James A., Standish, Christopher D., Foster, Gavin L. and Ezard, Thomas H. G.
(2023)
Laser ablation mass spectrometry blast through detection in R.
Rapid Communications in Mass Spectrometry, 37 (15), , [e9533].
(doi:10.1002/rcm.9533).
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 algorithmically identifying 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.
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Rapid Comm Mass Spectrometry - 2023 - Searle‐Barnes - Laser ablation mass spectrometry blast through detection in R (1)
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Accepted/In Press date: 28 April 2023
e-pub ahead of print date: 1 May 2023
Published date: 15 August 2023
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© 2023 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.
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Local EPrints ID: 477584
URI: http://eprints.soton.ac.uk/id/eprint/477584
ISSN: 0951-4198
PURE UUID: ed09c6b9-7691-4380-9fad-4c4617d66a04
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Date deposited: 08 Jun 2023 16:56
Last modified: 17 Mar 2024 03:48
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Author:
Thomas H. G. Ezard
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