patRoon: Open source software platform for environmental mass spectrometry based non-target screening
Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailored and straightforward non-target analysis workflows. This platform makes the use, evaluation and mixing of well-tested algorithms seamless by harmonizing various common (primarily open) software tools under a consistent interface. In addition, patRoon offers various functionality and strategies to simplify and perform automated processing of complex (environmental) data effectively. patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform time-efficient and automated non-target data annotation of environmental samples is demonstrated with a simple and reproducible workflow using open-access data of spiked samples from a drinking water treatment plant study. In addition, the ability to easily use, combine and evaluate different algorithms was demonstrated for three commonly used feature finding algorithms. This article, combined with already published works, demonstrate that patRoon helps make comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.
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Posted 04 Nov, 2020
On 06 Jan, 2021
On 22 Nov, 2020
Received 12 Nov, 2020
On 30 Oct, 2020
On 29 Oct, 2020
Invitations sent on 29 Oct, 2020
On 29 Oct, 2020
Received 29 Oct, 2020
On 28 Oct, 2020
On 28 Oct, 2020
On 01 Oct, 2020
Received 20 Sep, 2020
Received 20 Sep, 2020
Invitations sent on 14 Sep, 2020
On 14 Sep, 2020
On 14 Sep, 2020
On 20 Jun, 2020
On 19 Jun, 2020
On 19 Jun, 2020
On 19 Jun, 2020
patRoon: Open source software platform for environmental mass spectrometry based non-target screening
Posted 04 Nov, 2020
On 06 Jan, 2021
On 22 Nov, 2020
Received 12 Nov, 2020
On 30 Oct, 2020
On 29 Oct, 2020
Invitations sent on 29 Oct, 2020
On 29 Oct, 2020
Received 29 Oct, 2020
On 28 Oct, 2020
On 28 Oct, 2020
On 01 Oct, 2020
Received 20 Sep, 2020
Received 20 Sep, 2020
Invitations sent on 14 Sep, 2020
On 14 Sep, 2020
On 14 Sep, 2020
On 20 Jun, 2020
On 19 Jun, 2020
On 19 Jun, 2020
On 19 Jun, 2020
Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processing software either lack functionality for environmental sciences, solve only part of the workflow, are not openly available and/or are restricted in input data formats. In this paper we present patRoon, a new R based open-source software platform, which provides comprehensive, fully tailored and straightforward non-target analysis workflows. This platform makes the use, evaluation and mixing of well-tested algorithms seamless by harmonizing various common (primarily open) software tools under a consistent interface. In addition, patRoon offers various functionality and strategies to simplify and perform automated processing of complex (environmental) data effectively. patRoon implements several effective optimization strategies to significantly reduce computational times. The ability of patRoon to perform time-efficient and automated non-target data annotation of environmental samples is demonstrated with a simple and reproducible workflow using open-access data of spiked samples from a drinking water treatment plant study. In addition, the ability to easily use, combine and evaluate different algorithms was demonstrated for three commonly used feature finding algorithms. This article, combined with already published works, demonstrate that patRoon helps make comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the manuscript can be downloaded and accessed as a PDF.