Reference : patRoon: open source software platform for environmental mass spectrometry based non-...
Scientific journals : Article
Life sciences : Environmental sciences & ecology
http://hdl.handle.net/10993/46662
patRoon: open source software platform for environmental mass spectrometry based non-target screening
English
Helmus, Rick [> >]
ter Laak, Thomas L. [> >]
van Wezel, Annemarie P. [> >]
de Voogt, Pim [> >]
Schymanski, Emma mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Jan-2021
Journal of Cheminformatics
13
1
1
Yes (verified by ORBilu)
International
1758-2946
[en] Abstract 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.
Luxembourg Centre for Systems Biomedicine (LCSB): Environmental Cheminformatics (Schymanski Group)
Fonds National de la Recherche - FnR
ECHIDNA
Researchers ; Professionals ; Students
http://hdl.handle.net/10993/46662
10.1186/s13321-020-00477-w
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00477-w
All rights reserved
FnR ; FNR12341006 > Emma Schymanski > ECHIDNA > Environmental Cheminformatics To Identify Unknown Chemicals And Their Effects > 01/10/2018 > 30/09/2023 > 2018

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