Integration of target analyses, non-target screening and effect-based monitoring to assess OMP related water quality changes in drinking water treatment

Brunner, Andrea M.; Bertelkamp, C.; Dingemans, Milou M.L.; Kolkman, Annemieke; Wols, B.A.; Harmsen, D.J.H.; Siegers, W.G.; Martijn, Bram J.; Oorthuizen, Wim A.; Laak, Thomas L. ter

doi:10.1016/j.scitotenv.2019.135779

Cited by 61 publications

(43 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The Further analytical conditions are as described in [11]. The raw data files can be obtained from [107].…”

Section: Benchmark and Demonstration Datamentioning

confidence: 99%

“…was used for the patRoon demonstration. The list was based on the detected compounds reported in [11], and SMILES identifiers for each suspect were collected from PubChem [23].…”

Section: Competing Interestsmentioning

confidence: 99%

“…Recent technological advancements in chromatography and high resolution MS (HRMS) allows detection and tentative identification of compounds without the prior need of standards [1]. This 'non-target' analysis (NTA) approach is increasingly adopted to perform simultaneous screening of up to thousands of chemicals in the environment, such as finding new CEC [1][2][3][4][5][6], identifying chemical transformation (by)products [7][8][9][10][11][12] and identification of toxicants in the environment [13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Patroon: Open Source Software Platform for Environmental Mass Spectrometry Based Non-target Screening

Helmus

Laak

Voogt

et al. 2020

Preprint

View full text Add to dashboard Cite

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 tailoredand straightforwardnon-target analysis workflows. This platform makes the usage, evaluation and mixing of well-tested algorithms seamless by harmonizing various commonly (primarily open) software tools under a consistent interface. In addition, patRoonoffersvarious functionality and strategies tosimplify 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 a straightforward and effective non-target analysis was demonstrated with real-world environmental samples, showing thatpatRoonmakes comprehensive (environmental) non-target analysis readily accessible to a wider community of researchers.

show abstract

“…The Further analytical conditions are as described in [11]. The raw data files can be obtained from [107].…”

Section: Benchmark and Demonstration Datamentioning

confidence: 99%

“…was used for the patRoon demonstration. The list was based on the detected compounds reported in [11], and SMILES identifiers for each suspect were collected from PubChem [23].…”

Section: Competing Interestsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Patroon: Open Source Software Platform for Environmental Mass Spectrometry Based Non-target Screening

Helmus

Laak

Voogt

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The analyses were performed using an LC-HRMS Orbitrap Fusion system (ThermoFisher Scientific, Bremen, Germany) operating with positive electrospray ionization. Further details of the pilot installations and analytical conditions are described in [11]. The raw data files can be obtained from [111].…”

Section: Benchmark and Demonstration Datamentioning

confidence: 99%

“…Recent technological advancements in chromatography and high resolution MS (HRMS) allows detection and tentative identification of compounds without the prior need of standards [1]. This 'non-target' analysis (NTA) approach is increasingly adopted to perform simultaneous screening of up to thousands of chemicals in the environment, such as finding new CECs [1][2][3][4][5][6], identifying chemical transformation (by)products [7][8][9][10][11][12] and identification of toxicants in the environment [13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

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

Helmus

Laak

Wezel

et al. 2020

Preprint

View full text Add to dashboard Cite

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.

show abstract

The role of effect-based methods to address water quality monitoring in South Africa: a developing country’s struggle

Kruger

Pieters

Horn

et al. 2022

Environ Sci Pollut Res

View full text Add to dashboard Cite

Water is an important resource, and it is a worldwide struggle to provide water of good quality to the whole population. Despite good governing laws and guidelines set in place to help protect the water resources and ensure it is of good quality for various consumers, the water quality in South Africa is worsening due to lack of management. The deteriorating infrastructure is becoming progressively worse, due to corruption and insufficient funds. The ever-increasing number of toxicants, as well as the identification of emerging chemicals of concern, are also challenges South Africa is facing. Chemical analysis cannot determine the total biological effect of a mixture of chemical compounds, but this shortcoming can be addressed by adding effect-based methods (EBMs) to water quality monitoring programmes. In this paper, the current status of water quality monitoring in South Africa is discussed, as well as the capacity of the country to add EBMs to its water quality monitoring programmes to protect and improve human and animal life. Graphical abstract Created in Biorender.com

show abstract

Integration of target analyses, non-target screening and effect-based monitoring to assess OMP related water quality changes in drinking water treatment

Cited by 61 publications

References 62 publications

Patroon: Open Source Software Platform for Environmental Mass Spectrometry Based Non-target Screening

Patroon: Open Source Software Platform for Environmental Mass Spectrometry Based Non-target Screening

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

The role of effect-based methods to address water quality monitoring in South Africa: a developing country’s struggle

Contact Info

Product

Resources

About