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See detailDevelopment and Application of an LC-MS/MS Untargeted Exposomics Method with a Separated Pooled Quality Control Strategy
Frigerio, Gianfranco UL; Moruzzi, Camilla; Mercadante, Rosa et al

in Molecules (2022), 27(8), 2580

Pooled quality controls (QCs) are usually implemented within untargeted methods to improve the quality of datasets by removing features either not detected or not reproducible. However, this approach can ... [more ▼]

Pooled quality controls (QCs) are usually implemented within untargeted methods to improve the quality of datasets by removing features either not detected or not reproducible. However, this approach can be limiting in exposomics studies conducted on groups of exposed and nonexposed subjects, as compounds present at low levels only in exposed subjects can be diluted and thus not detected in the pooled QC. The aim of this work is to develop and apply an untargeted workflow for human biomonitoring in urine samples, implementing a novel separated approach for preparing pooled quality controls. An LC-MS/MS workflow was developed and applied to a case study of smoking and non-smoking subjects. Three different pooled quality controls were prepared: mixing an aliquot from every sample (QC-T), only from non-smokers (QC-NS), and only from smokers (QC-S). The feature tables were filtered using QC-T (T-feature list), QC-S, and QC-NS, separately. The last two feature lists were merged (SNS-feature list). A higher number of features was obtained with the SNS-feature list than the T-feature list, resulting in identification of a higher number of biologically significant compounds. The separated pooled QC strategy implemented can improve the nontargeted human biomonitoring for groups of exposed and nonexposed subjects. [less ▲]

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See detailEnvironmental Detective Work: Environmental Cheminformatics and the Exposome
Schymanski, Emma UL

Presentation (2022, January 10)

The multitude of chemicals to which we are exposed is ever increasing, with over 110 million chemicals in the largest open chemical databases, over 350,000 in global use inventories, and over 70,000 ... [more ▼]

The multitude of chemicals to which we are exposed is ever increasing, with over 110 million chemicals in the largest open chemical databases, over 350,000 in global use inventories, and over 70,000 estimated to be in household use alone. Detectable molecules in exposomics can be captured using non-target high resolution mass spectrometry (HRMS), but despite the size of the chemical space, scientists cannot yet identify most of the tens of thousands of features in each sample, leading to critical bottlenecks in identification and data interpretation. This talk will cover European and worldwide community initiatives and resources to help connect environmental expert knowledge and observations towards a better understanding of the exposome, including various open cheminformatics and computational mass spectrometry approaches such as the NORMAN Suspect List Exchange, MassBank, MetFrag and PubChemLite for Exposomics. [less ▲]

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See detailDiscovering pesticides and their TPs in Luxembourg waters using open cheminformatics approaches
Krier, Jessy; Singh, Randolph R.; Kondic, Todor UL et al

in Environment International (2022), 158

The diversity of hundreds of thousands of potential organic pollutants and the lack of (publicly available) information about many of them is a huge challenge for environmental sciences, engineering, and ... [more ▼]

The diversity of hundreds of thousands of potential organic pollutants and the lack of (publicly available) information about many of them is a huge challenge for environmental sciences, engineering, and regulation. Suspect screening based on high-resolution liquid chromatography-mass spectrometry (LC-HRMS) has enormous potential to help characterize the presence of these chemicals in our environment, enabling the detection of known and newly emerging pollutants, as well as their potential transformation products (TPs). Here, suspect list creation (focusing on pesticides relevant for Luxembourg, incorporating data sources in 4 languages) was coupled to an automated retrieval of related TPs from PubChem based on high confidence suspect hits, to screen for pesticides and their TPs in Luxembourgish river samples. A computational workflow was established to combine LC-HRMS analysis and pre-screening of the suspects (including automated quality control steps), with spectral annotation to determine which pesticides and, in a second step, their related TPs may be present in the samples. The data analysis with Shinyscreen (https://gitlab.lcsb.uni.lu/eci/shinyscreen/), an open source software developed in house, coupled with custom-made scripts, revealed the presence of 162 potential pesticide masses and 96 potential TP masses in the samples. Further identification of these mass matches was performed using the open source approach MetFrag (https://msbi.ipb-halle.de/MetFrag/). Eventual target analysis of 36 suspects resulted in 31 pesticides and TPs confirmed at Level-1 (highest confidence), and five pesticides and TPs not confirmed due to different retention times. Spatio-temporal analysis of the results showed that TPs and pesticides followed similar trends, with a maximum number of potential detections in July. The highest detections were in the rivers Alzette and Mess and the lowest in the Sûre and Eisch. This study (a) added pesticides, classification information and related TPs into the open domain, (b) developed automated open source retrieval methods - both enhancing FAIRness (Findability, Accessibility, Interoperability and Reusability) of the data and methods; and (c) will directly support “L’Administration de la Gestion de l’Eau” on further monitoring steps in Luxembourg. [less ▲]

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See detailOne planet: one health. A call to support the initiative on a global science–policy body on chemicals and waste
Brack, Werner; Barcelo Culleres, Damia; Boxall, Alistair B. A. et al

in Environmental Sciences Europe (2022), 34(1), 21

Abstract The chemical pollution crisis severely threatens human and environmental health globally. To tackle this challenge the establishment of an overarching international science–policy body has ... [more ▼]

Abstract The chemical pollution crisis severely threatens human and environmental health globally. To tackle this challenge the establishment of an overarching international science–policy body has recently been suggested. We strongly support this initiative based on the awareness that humanity has already likely left the safe operating space within planetary boundaries for novel entities including chemical pollution. Immediate action is essential and needs to be informed by sound scientific knowledge and data compiled and critically evaluated by an overarching science–policy interface body. Major challenges for such a body are (i) to foster global knowledge production on exposure, impacts and governance going beyond data-rich regions (e.g., Europe and North America), (ii) to cover the entirety of hazardous chemicals, mixtures and wastes, (iii) to follow a one-health perspective considering the risks posed by chemicals and waste on ecosystem and human health, and (iv) to strive for solution-oriented assessments based on systems thinking. Based on multiple evidence on urgent action on a global scale, we call scientists and practitioners to mobilize their scientific networks and to intensify science–policy interaction with national governments to support the negotiations on the establishment of an intergovernmental body based on scientific knowledge explaining the anticipated benefit for human and environmental health. [less ▲]

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See detailpatRoon 2.0: Improved non-target analysis workflows including automated transformation product screening
Helmus, Rick; van de Velde, Bas; Brunner, Andrea M. et al

in Journal of Open Source Software (2022), 7(71), 4029

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 ... [more ▼]

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). [less ▲]

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See detailHistorical Exposomics and High Resolution Mass Spectrometry
Aurich, Dagny UL; Miles, Owen; Schymanski, Emma UL

in Exposome (2021), 00(0),

Awareness of the exposome and its influence on health has increased in the last decade. As past exposures can cause changes in human health many years later, delving into the past is relevant for both ... [more ▼]

Awareness of the exposome and its influence on health has increased in the last decade. As past exposures can cause changes in human health many years later, delving into the past is relevant for both diagnostic and prevention purposes, but remains a challenging task. Lifestyle, diet, and socioeconomic information of the past should be well documented and compatible with modern data science methods. While chemical analysis nowadays makes use of high resolution mass spectrometry (HR-MS) for highly sensitive and comprehensive coverage of samples plus retrospective analysis, these data archives are in the very early stages. Since past measurements are often only available for a limited set of chemicals, adding to this knowledge requires careful selection of sample types and sampling sites, which may not always be available. The choice of analytes and analytical methods should be suitable for the study question —which is not always clear in advance in exposomics. Data interpretation and the use of appropriate databases are indispensable for a proper exposure assessment, and as databases and knowledge grow, re-analysis of physically or digitally archived samples could enable “continuous monitoring” efforts. This review focuses on the chemical analytical approaches necessary to capture the complexity of the historical exposome. Various sample types, analytes as well as analyses and data interpretation methods are discussed in relation to chemical exposures, while the connection to health remains in focus. It ends with perspectives and challenges in assessing the historical exposome, discussing how we can “learn from the past” to build a better future. [less ▲]

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See detailFinding Small Molecules and their Metabolites in Big Data
Schymanski, Emma UL

Presentation (2021, December 15)

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See detailExploring the Exposomewith HPC
Schymanski, Emma UL

Presentation (2021, November 10)

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See detailEmerging Contaminants, Cheminformatics, Mass Spectrometry and the Exposome
Schymanski, Emma UL

Presentation (2021, October 26)

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See detailChemical contamination of the sea – (management of the knowns and) Research on the unknowns
Schymanski, Emma UL

Scientific Conference (2021, October 20)

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See detailHarnessing the Exposome, Cheminformatics and Mass Spectrometry for Clinical Metabolomics
Schymanski, Emma UL

Scientific Conference (2021, September 14)

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See detailUpdate on NORMAN-SusDat NORMAN-SLE (Suspect List Exchange)
Schymanski, Emma UL

Scientific Conference (2021, September 14)

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See detailIdentifying Exposome Chemicals: Measured Data Metadata, Metabolism and More …
Schymanski, Emma UL

Scientific Conference (2021, September 10)

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See detailCheminformatics and Mass Spectrometry meets Clinical Metabolomics
Schymanski, Emma UL

Scientific Conference (2021, September 01)

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See detailExposome Boot Camp PubChemLite Lab: Cheminformatics for the Exposome
Schymanski, Emma UL

Presentation (2021, July 23)

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See detailFAIR chemical structures in the Journal of Cheminformatics
Schymanski, Emma UL; Bolton, Evan E.

in Journal of Cheminformatics (2021), 13(1), 50

Abstract The ability to access chemical information openly is an essential part of many scientific disciplines. The Journal of Cheminformatics is leading the way for rigorous, open cheminformatics in many ... [more ▼]

Abstract The ability to access chemical information openly is an essential part of many scientific disciplines. The Journal of Cheminformatics is leading the way for rigorous, open cheminformatics in many ways, but there remains room for improvement in primary areas. This letter discusses how both authors and the journal alike can help increase the FAIR ness (Findability, Accessibility, Interoperability, Reusability) of the chemical structural information in the journal. A proposed chemical structure template can serve as an interoperable Additional File format (already accessible ), made more findable by linking the DOI of this data file to the article DOI metadata, supporting further reuse . [less ▲]

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See detailDiscovering Pesticides, Pharmaceuticals TPs in Luxembourg Waters using Open Cheminformatics Approaches
Krier, Jessy; Singh, Randolph R.; Kondic, Todor UL et al

Scientific Conference (2021, June 24)

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See detailOpen Science @LCSB-ECI
Schymanski, Emma UL

Presentation (2021, June 17)

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See detailDefining a Manageable, Dynamic Chemical Space for Exposomics
Schymanski, Emma UL

Scientific Conference (2021, April 27)

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