Helmus Rick, Ter Laak Thomas L, van Wezel Annemarie P, de Voogt Pim, Schymanski Emma L
Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.
KWR Water Research Institute, Chemical Water Quality and Health, P.O. Box 1072, 3430 BB, Nieuwegein, The Netherlands.
J Cheminform. 2021 Jan 6;13(1):1. doi: 10.1186/s13321-020-00477-w.
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.
基于质谱的非靶向分析在环境科学中越来越多地被采用，用于在高度复杂的样品中同时筛选和识别多种化学物质。然而，当前的数据处理软件要么缺乏针对环境科学的功能，只能解决部分工作流程，要么不是开源的，和/或在输入数据格式上受到限制。在本文中，我们介绍了patRoon，这是一个基于R的新型开源软件平台，它提供了全面、完全定制且简单直接的非靶向分析工作流程。该平台通过在一致的界面下整合各种经过充分测试的（主要是开源的）软件工具，使经过充分测试的算法的使用、评估和混合变得无缝。此外，patRoon提供了各种功能和策略，以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。通过使用来自饮用水处理厂研究的加标样品的开放获取数据，以简单且可重复的工作流程展示了patRoon对环境样品进行高效且自动化的非靶向数据注释的能力。此外，还针对三种常用的特征发现算法展示了轻松使用、组合和评估不同算法的能力。本文与已发表的作品相结合，证明了patRoon有助于使更广泛的研究人员群体能够轻松进行全面的（环境）非靶向分析。
