Discovering pesticides and their TPs in Luxembourg waters using open cheminformatics approaches

Krier, Jessy; Singh, Randolph R.; Kondić, Todor; Lai, Adelene; Diderich, Philippe; Zhang, Jian; Thiessen, Paul A.; Bolton, Evan; Schymanski, Emma L.

doi:10.1016/j.envint.2021.106885

Cited by 33 publications

(29 citation statements)

References 27 publications

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“…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 ].…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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Background The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101). Conclusions The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/).

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Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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“…Parents for (B) are specified from (1) a target list, (2) results of a suspect screening to find parents by mass, or (3) candidates of feature compound annotation (see ). Corresponding TP structures are then either obtained in silico with BioTransformer (Djoumbou-Feunang et al, 2019), or through a library search from PubChem data (Kim, 2021;Krier et al, 2022;Schymanski, Kondić, et al, 2021; or a custommade library. Metabolic logic (C), which does not depend on parent structural data, uses transformation reactions from Schollée et al (2015) or a custom-made list.…”

Section: New Functionality Transformation Product Screening Workflowmentioning

confidence: 99%

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

Helmus¹,

Velde²,

Brunner³

et al. 2022

JOSS

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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.

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“…Transformations for 5135 CIDs have been added from the datasets S60 SWISSPEST19 [129], S66 EAWAGTPS [163], S68 HSDBTPS [205], S73 METXBIODB [110], S74 REFTPS [71], S78 SLUPESTTPS [173] and S79 UACCSCEC [187], as described in some of the articles mentioned above [24,174,241]. As a part of this, SEO text snippets describing these relationships have been added to the following headings: Metabolism/Metabolites (S73 METXBIODB [110] and S82 THSTPS [227]), Drug Transformations (S66 EAWAGTPS [163]) and Agrochemical Transformations (S60 SWISSPEST19 [129], S66 EAWAGTPS [163] and S78 SLUPESTTPS [173]).…”

Section: Norman-sle Pubchem Integrationmentioning

confidence: 99%

“…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].…”

Section: Fair Data and Chemical Curationmentioning

confidence: 99%

See 1 more Smart Citation

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

Taha

Aalizadeh

Alygizakis

et al. 2022

Preprint

Self Cite

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Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per-and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of >40,000 unique views, >50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101). Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one chemical, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/).

show abstract

Discovering pesticides and their TPs in Luxembourg waters using open cheminformatics approaches

Cited by 33 publications

References 27 publications

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

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

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

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