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

Abstract

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 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).Helmus et al. ( 2022). patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening.

The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

“…A large focus has been placed on TPs over the recent years. A continuation of ongoing efforts will include adding more TPs, including the extraction of data from literature to fill data gaps [ 71 , 174 , 205 ] and the integration of workflows in patRoon [ 257 ] in a manner compatible with other NTS workflows. Over the years, there has been increasing interest to add lists of predicted TPs to the NORMAN-SLE, with submissions including predicted TPs for S6 ITNANTIBIOTICS [ 159 ], S71 CECSCREEN [ 85 ] (both generated with BioTransformer [ 111 ]) and S38 SOLNSLMCTPS [ 102 ].…”

“…5 . The Transformations data are compiled and archived on GitLab [ 80 ] and Zenodo [ 256 ], and is integrated in patRoon 2.0 [ 257 ], an open source software for mass spectrometry based non-target analysis that includes suspect and transformation product screening workflows.…”

Studying the Parkinson’s disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study

“…Next, relevant MS data was extracted using the mzR algorithms [50]. Molecular formulas were calculated using GenForm [29,51,52], and compound identification was performed with MetFrag (MetFrag2.4.5-CL jar file) [31] and the PubChemLite for Exposomics (PCL) database [53]. Additionally, different databases and suspect lists were used, as described below in the "10" section.…”

“…MS-DIAL is a software pipeline that allows the identification and quantification of small molecules by mass spectral deconvolution [27]. The software platform patRoon [28,29] provides comprehensive, fully tailored non-target analysis workflows in R, harmonizing many available tools and approaches. MetFrag supports compound identification including in silico fragmentation, matching experimental data with mass spectrometry databases like MoNA and additional metadata along with other features [30,31].…”

The NORMAN Suspect List Exchange (NORMAN-SLE): Facilitating European and Worldwide Collaboration on Suspect Screening in High Resolution Mass Spectrometry

“…A large focus has been placed on TPs over the recent years. A continuation of ongoing efforts will include adding more TPs, including the extraction of data from literature to ll data gaps [71,174,205] and the integration of work ows in patRoon [257] in a manner compatible with other NTS work ows. Over the years, there has been increasing interest to add lists of predicted TPs to the NORMAN-SLE, with submissions including predicted TPs for S6 ITNANTIBIOTICS [159], S71 CECSCREEN [85] (both generated with BioTransformer [111]) and S38 SOLNSLMCTPS [102].…”