Examining NTA performance and potential using fortified and reference house dust as part of EPA’s Non-Targeted Analysis Collaborative Trial (ENTACT)

Newton, Seth; Sobus, Jon R.; Ulrich, Elin M.; Singh, Randolph R.; Chao, Alex; McCord, James; Laughlin-Toth, Sarah; Strynar, Mark J.

doi:10.1007/s00216-020-02658-w

Cited by 28 publications

(21 citation statements)

References 28 publications

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“…To meet this challenge, the community should push for (1) open sharing of raw NTA data so new computational approaches can be compared using identical data, (2) additional assessment studies of blinded samples with known composition (akin to ENTACT 39,40 and CASMI 41 ), (3) adoption of common reporting formats and transparent sharing of metadata, (4) adoption of common QA/QC practices, and (5) the development of comparison tools to support automated performance assessment. Additionally, the NTA community would benefit from a better understanding of the relationship between identification confidence and false discovery rates or the probability of presence.…”

Section: Discussionmentioning

confidence: 99%

“…Such assessments can require running samples on multiple instruments or through multiple data analysis pipelines, yielding both time and cost considerations. To meet this challenge, the community should push for (1) open sharing of raw NTA data so new computational approaches can be compared using identical data, (2) additional assessment studies of blinded samples with known composition (akin to ENTACT , and CASMI), (3) adoption of common reporting formats and transparent sharing of metadata, (4) adoption of common QA/QC practices, and (5) the development of comparison tools to support automated performance assessment.…”

Section: Challenges Recommendations and Outlookmentioning

confidence: 99%

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An Introduction to the Benchmarking and Publications for Non-Targeted Analysis Working Group

et al. 2021

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Non-targeted analysis (NTA) encompasses a rapidly evolving set of mass spectrometry techniques aimed at characterizing the chemical composition of complex samples, identifying unknown compounds, and/or classifying samples, without prior knowledge regarding the chemical content of the samples. Recent advances in NTA are the result of improved and more accessible instrumentation for data generation and analysis tools for data evaluation and interpretation. As researchers continue to develop NTA approaches in various scientific fields, there is a growing need to identify, disseminate, and adopt community-wide method reporting guidelines. In 2018, NTA researchers formed the Benchmarking and Publications for Non-Targeted Analysis Working Group (BP4NTA) to address this need. Consisting of participants from around the world and representing fields ranging from environmental science and food chemistry to 'omics and toxicology, BP4NTA provides resources addressing a variety of challenges associated with NTA. Thus far, BP4NTA group members have aimed to establish a consensus on NTA-related terms and concepts and to create consistency in reporting practices by providing resources on a public Web site, including consensus definitions, reference content, and lists of available tools. Moving forward, BP4NTA will provide a setting for NTA researchers to continue discussing emerging challenges and contribute to additional harmonization efforts.

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Section: Discussionmentioning

confidence: 99%

Section: Challenges Recommendations and Outlookmentioning

confidence: 99%

An Introduction to the Benchmarking and Publications for Non-Targeted Analysis Working Group

et al. 2021

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“…Still, the results from this demonstration indicates that each algorithm generates unique results. Dedicated efforts such as ENTACT [120][121][122] will help to unravel the importance of unique and overlapping algorithm results, however, such studies are out of the scope of this article. Regardless, this demonstration showed how patRoon provides researchers the tools needed to easily use and combine workflow data from different algorithms to perform such an evaluation for their use cases.…”

Section: Demonstration: Algorithm Consensus 664mentioning

confidence: 99%

patRoon: Open source software platform for environmental mass spectrometry based non-target screening

Helmus

Laak

Wezel

et al. 2020

Preprint

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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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“…Although significant efforts have been made to improve and standardize NTA of environmental samples (Newton et al, 2020;Schymanski et al, 2014Schymanski et al, , 2015Sobus et al, 2019), what has been somewhat overlooked is the importance of the sampling regime itself in obtaining a more accurate representation of the overall contamination burden in a specific aquatic ecosystem. Accurate representation of the temporal variation of substance loading/concentrations necessitates nearly continuous monitoring; however, in most cases this cannot be achieved due to a variety of well-known methodological, logistical, and cost constraints.…”

Section: Introductionmentioning

confidence: 99%

Monitoring of Environmental Contaminants in Mixed‐Use Watersheds Combining Targeted and Nontargeted Analysis with Passive Sampling

Renaud

Sabourin

Hoogstra

et al. 2021

Enviro Toxic and Chemistry

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Understanding the environmental fate, transport, and occurrence of pesticides and pharmaceuticals in aquatic environments is of utmost concern to regulators. Traditionally, monitoring of environmental contaminants in surface water has consisted of liquid chromatography-tandem mass spectrometry analyses for a set of targeted compounds in discrete samples. These targeted approaches are limited by the fact that they only provide information on compounds within a target list present at the time and location of sampling. To address these limitations, there has been considerable interest in suspect screening and nontargeted analysis (NTA), which allow for the detection of all ionizable compounds in the sample with the added benefit of data archiving for retrospective mining. Even though NTA can detect a large number of contaminants, discrete samples only provide a snapshot perspective of the chemical disposition of an aquatic environment at the time of sampling, potentially missing episodic events. We evaluated two types of passive chemical samplers for nontargeted analysis in mixed-use watersheds. Nontargeted data were processed using MS-DIAL to screen against our in-house library and public databases of more than 1300 compounds. The data showed that polar organic chemicals integrative samplers (POCIS) were able to capture the largest number of analytes with better reproducibility than organic compound-diffusive gradients in thin film (o-DGT), resulting from the greater amount of binding sorbent. We also showed that NTA combined with passive sampling gives a more representative picture of the contaminants present at a given site and enhances the ability to identify the nature of point and nonpoint pollution sources and ecotoxicological impacts.

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Examining NTA performance and potential using fortified and reference house dust as part of EPA’s Non-Targeted Analysis Collaborative Trial (ENTACT)

Cited by 28 publications

References 28 publications

An Introduction to the Benchmarking and Publications for Non-Targeted Analysis Working Group

An Introduction to the Benchmarking and Publications for Non-Targeted Analysis Working Group

patRoon: Open source software platform for environmental mass spectrometry based non-target screening

Monitoring of Environmental Contaminants in Mixed‐Use Watersheds Combining Targeted and Nontargeted Analysis with Passive Sampling

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