patRoon: open source software platform for environmental mass spectrometry based non-target screening.
patRoon: open source software platform for environmental mass spectrometry based non-target screening.
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DOI：
10.1186/s13321-020-00477-w
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发表时间：
2021-01-06
影响因子：
8.6
通讯作者：
Schymanski EL
中科院分区：
文献类型：
--
作者：
Helmus R;Ter Laak TL;van Wezel AP;de Voogt P;Schymanski EL
基于质谱学的非目标分析在环境科学中越来越多地被采用，以在高度复杂的样品中同时筛选和鉴定大量化学物质。然而，目前的数据处理软件要么缺乏环境科学的功能，只解决部分工作流程，要么不公开可用，和/或受到输入数据格式的限制。本文介绍了Patroon，一个新的基于R的开源软件平台，它提供了全面的、完全定制的和直接的非目标分析工作流。该平台通过在一致的界面下协调各种常见(主要是开放的)软件工具，使经过良好测试的算法的使用、评估和混合变得无缝。此外，Patroon还提供各种功能和策略，可有效简化和执行复杂(环境)数据的自动化处理。Patroon实施了几种有效的优化策略，以显著减少计算时间。Patroon通过一个简单且可重现的工作流程展示了Patroon对环境样本执行省时且自动化的非目标数据注释的能力，该工作流程使用来自饮用水处理厂研究的添加样本的开放访问数据。此外，还对三种常用的特征发现算法进行了简单的使用、组合和评估。这篇文章，结合已经发表的作品，展示了Patroon帮助使更广泛的研究人员社区容易地获得全面的(环境)非目标分析。
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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影响因子：
8.6
作者：
Djoumbou-Feunang, Yannick;Fiamoncini, Jarlei;Wishart, David S.
通讯作者：
Wishart, David S.
影响因子：
8.6
作者：
Blaženović I;Kind T;Torbašinović H;Obrenović S;Mehta SS;Tsugawa H;Wermuth T;Schauer N;Jahn M;Biedendieck R;Jahn D;Fiehn O
通讯作者：
Fiehn O
影响因子：
14.9
作者：
Allen F;Pon A;Wilson M;Greiner R;Wishart D
通讯作者：
Wishart D
影响因子：
11.8
作者：
Collet, Berenice;van Vugt-Lussenburg, Barbara M. A.;van der Burg, Bart
通讯作者：
van der Burg, Bart
影响因子：
7.4
作者：
Broeckling, C. D.;Afsar, F. A.;Prenni, J. E.
通讯作者：
Prenni, J. E.