patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening

Non-target analysis (NTA) via chromatography coupled to high resolution mass spectrometry (HRMS) is used to monitor and identify organic chemicals in the environment. Biotic and abiotic processes can transform original chemicals (parents) into transformation products (TPs). These TPs can be of equal or more concern than their parent compounds and are therefore critical to monitor and identify in the environment (Escher & Fenner, 2011; Farré et al., 2008), often with NTA. Given the amount of data generated by NTA, advanced automated data processing workflows are essential. The open source, R-based (R Core Team, 2021) platform patRoon (Helmus, ter Laak, et al., 2021) offers automated, straightforward, flexible and comprehensive NTA workflows.

This article describes improvements introduced in patRoon 2.0, including extensive TP screening and simultaneous processing of positive and negative HRMS data. The updated documentation and code are available via https://rickhelmus.github.io/patRoon and archived in Helmus, Velde, et al. (2021).