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See detailDigital Detective Work: Connecting Cheminformatics, Mass Spectrometry and our Environment (analytica Conference)
Schymanski, Emma UL; Bolton, Evan

Scientific Conference (2020, October 20)

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See detailData Science and Environmental Cheminformatics (SanDAL Workshop, Uni Lu)
Schymanski, Emma UL

Presentation (2020, October 13)

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See detailMeasuring the Environmental Exposome (ISES2020)
Schymanski, Emma UL

Scientific Conference (2020, September 21)

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See detailSchadstoffen auf der Spur mit Umweltcheminformatik
Schymanski, Emma UL

Scientific Conference (2020, September 17)

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See detailMetFrag: Annotating "Unknowns" - Exposome Boot Camp 2020 Virtual Edition
Schymanski, Emma UL

Presentation (2020, July 24)

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See detailFinding Small Molecules (and PFAS) with High Resolution Mass Spectrometry
Schymanski, Emma UL

Presentation (2020, May 05)

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See detailInteractive MS/MS Visualization with the Metabolomics Spectrum Resolver Web Service
Wang, Mingxun; Rogers, Simon; Bittremieux, Wout et al

E-print/Working paper (2020)

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See detailMining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced Fragmentation
Ludwig, Marcus; Broeckling, Corey D.; Dorrestein, Pieter et al

E-print/Working paper (2020)

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See detailVirtual Podium Keynote: Compound Identification and Exposomics: DIY Databases?
Schymanski, Emma UL; Bolton, Evan; Helmus, Rick et al

Presentation (2020, April 10)

In light of recent events, many of us have been impacted by the cancellation of conferences and meetings. We are not only losing the opportunity to present our research, but a chance to connect with our ... [more ▼]

In light of recent events, many of us have been impacted by the cancellation of conferences and meetings. We are not only losing the opportunity to present our research, but a chance to connect with our community. Virtual Podium is a platform and opportunity to present and learn about compelling scientific research. Our third session will be focused on Compound Identification. Our keynote speaker this week will be Emma Schymanski who is the PI of Environmental Cheminformatics at the University of Luxembourg. Session 3: Compound Identification Friday, April 10, 2020 at 12:00-1:00PM PDT (3:00-4:00PM EDT) Session 3 - Compound Identification: https://www.eventbrite.com/e/101426613732 [less ▲]

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See detailEnvironmental Cheminformatics: Case study of Thirdhand Smoke in House Dust
Schymanski, Emma UL; Torres, Sonia; Ramirez, Noeia

Presentation (2020, January 23)

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See detailEvaluation of reverse osmosis drinking water treatment of riverbank filtrate using bioanalytical tools and non-target screening
Albergamo, Vittorio; Escher, Beate I.; Schymanski, Emma UL et al

in Environmental Science: Water Research and Technology (2020), 6(1), 103--116

Stand-alone reverse osmosis (RO) has been proposed to produce high-quality drinking water from raw riverbank filtrate impacted by anthropogenic activities. To evaluate RO efficacy in removing organic ... [more ▼]

Stand-alone reverse osmosis (RO) has been proposed to produce high-quality drinking water from raw riverbank filtrate impacted by anthropogenic activities. To evaluate RO efficacy in removing organic micropollutants, biological analyses were combined with non-target screening using high-resolution mass spectrometry and open cheminformatics tools. The bank filtrate induced xenobiotic metabolism mediated by the aryl hydrocarbon receptor AhR, adaptive stress response mediated by the transcription factor Nrf2 and genotoxicity in the Ames-fluctuation test. These effects were absent in the RO permeate (product water), indicating the removal of bioactive micropollutants by RO membranes. In the water samples, 49 potentially toxic compounds were tentatively identified with the in silico fragmentation tool MetFrag using the US Environmental Protection Agency CompTox Chemicals Dashboard database. 5 compounds were confirmed with reference standards and 16 were tentatively identified with high confidence based on similarities to accurate mass spectra in open libraries. The bioactivity data of the confirmed chemicals indicated that 2,6-dichlorobenzamide and bentazone in water samples can contribute to the activation of AhR and oxidative stress response, respectively. The bioactivity data of 7 compounds tentatively identified with high confidence indicated that these structures can contribute to the induction of such effects. This study showed that riverbank filtration followed by RO could produce drinking water free of the investigated toxic effects. [less ▲]

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See detailPubChemLite for Exposomics
Bolton, Evan; Schymanski, Emma UL; Kondic, Todor UL et al

Computer development (2020)

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See detailStudying Charge Migration Fragmentation of Sodiated Precursor Ions in Collision-Induced Dissociation at the Library Scale
Ludwig, Marcus; Broeckling, Corey D.; Dorrestein, Pieter C. et al

in Journal of the American Society for Mass Spectrometry (2020)

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See detailThe NORMAN Association and the European Partnership for Chemicals Risk Assessment (PARC): let’s cooperate!
Dulio, Valeria; Koschorreck, Jan; van Bavel, Bert et al

in Environmental Sciences Europe (2020), 32(1), 1--11

The Partnership for Chemicals Risk Assessment (PARC) is currently under development as a joint research and innovation programme to strengthen the scientific basis for chemical risk assessment in the EU ... [more ▼]

The Partnership for Chemicals Risk Assessment (PARC) is currently under development as a joint research and innovation programme to strengthen the scientific basis for chemical risk assessment in the EU. The plan is to bring chemical risk assessors and managers together with scientists to accelerate method development and the production of necessary data and knowledge, and to facilitate the transition to next-generation evidence-based risk assessment, a non-toxic environment and the European Green Deal. The NORMAN Network is an independent, well-established and competent network of more than 80 organisations in the field of emerging substances and has enormous potential to contribute to the implementation of the PARC partnership. NORMAN stands ready to provide expert advice to PARC, drawing on its long experience in the development, harmonisation and testing of advanced tools in relation to chemicals of emerging concern and in support of a European Early Warning System to unravel the risks of contaminants of emerging concern (CECs) and close the gap between research and innovation and regulatory processes. In this commentary we highlight the tools developed by NORMAN that we consider most relevant to supporting the PARC initiative: (i) joint data space and cutting-edge research tools for risk assessment of contaminants of emerging concern; (ii) collaborative European framework to improve data quality and comparability; (iii) advanced data analysis tools for a European early warning system and (iv) support to national and European chemical risk assessment thanks to harnessing, combining and sharing evidence and expertise on CECs. By combining the extensive knowledge and experience of the NORMAN network with the financial and policy-related strengths of the PARC initiative, a large step towards the goal of a non-toxic environment can be taken. [less ▲]

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See detailpatRoon: Open Source Software Platform for Environmental Mass Spectrometry Based Non-target Screening
Helmus, Rick; ter Laak, Thomas; van Wezel, Annemarie et al

E-print/Working paper (2020)

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See detailExpanded coverage of non-targeted LC-HRMS using atmospheric pressure chemical ionization: a case study with ENTACT mixtures.
Singh, Randolph UL; Chao, Alex; Phillips, Katherine A. et al

in Analytical and Bioanalytical Chemistry (2020)

Non-targeted analysis (NTA) is a rapidly evolving analytical technique with numerous opportunities to improve and expand instrumental and data analysis methods. In this work, NTA was performed on eight ... [more ▼]

Non-targeted analysis (NTA) is a rapidly evolving analytical technique with numerous opportunities to improve and expand instrumental and data analysis methods. In this work, NTA was performed on eight synthetic mixtures containing 1264 unique chemical substances from the U.S. Environmental Protection Agency’s Non-Targeted Analysis Collaborative Trial (ENTACT). These mixtures were analyzed by atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI) using both positive and negative polarities for a total of four modes. Out of the 1264 ENTACT chemical substances, 1116 were detected in at least one ionization mode, 185 chemicals were detected using all four ionization modes, whereas 148 were not detected. Forty-four chemicals were detected only by APCI, and 181 were detected only by ESI. Molecular descriptors and physicochemical properties were used to assess which ionization type was preferred for a given compound. One ToxPrint substructure (naphthalene group) was found to be enriched in compounds only detected using APCI, and eight ToxPrints (e.g., several alcohol moieties) were enriched in compounds only detected using ESI. Examination of physicochemical parameters for ENTACT chemicals suggests that those with higher aqueous solubility preferentially ionized by ESI−. While ESI typically detects a larger number of compounds, APCI offers chromatograms with less background, fewer co-elutions, and additional chemical space coverage, suggesting both should be considered for broader coverage in future NTA research. [less ▲]

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See detailComputational Metabolomics: From Cheminformatics to Machine Learning (Dagstuhl Seminar 20051)
Böcker, Sebastian; Broeckling, Corey; Schymanski, Emma UL et al

in Dagstuhl Reports (2020)

Dagstuhl Seminar 20051 on Computational Metabolomics is the third edition of seminars onthis topic and focused on Cheminformatics and Machine Learning. With the advent of higherprecision instrumentation ... [more ▼]

Dagstuhl Seminar 20051 on Computational Metabolomics is the third edition of seminars onthis topic and focused on Cheminformatics and Machine Learning. With the advent of higherprecision instrumentation, application of metabolomics to a wider variety of small molecules, andever increasing amounts of raw and processed data available, developments in cheminformaticsand machine learning are sorely needed to facilitate interoperability and leverage further insightsfrom these data. Following on from Seminars 17491 and 15492, this edition convened bothexperimental and computational experts, many of whom had attended the previous sessions andbrought much-valued perspective to the week’s proceedings and discussions. Throughout theweek, participants first debated on what topics to discuss in detail, before dispersing into smaller,focused working groups for more in-depth discussions. This dynamic format was found to bemost productive and ensured active engagement amongst the participants. The abstracts inthis report reflect these working group discussions, in addition to summarising several informalevening sessions. Action points to follow-up on after the seminar were also discussed, includingfuture workshops and possibly another Dagstuhl seminar in late 2021 or 2022. [less ▲]

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See detailA European proposal for quality control and quality assurance of tandem mass spectral libraries
Oberacher, Herbert; Sasse, Michael; Antignac, Jean-Philippe et al

in Environmental Sciences Europe (2020), 32(1), 1--19

Background: High resolution mass spectrometry (HRMS) is being used increasingly in the context of suspect and non-targeted screening for the identification of bioorganic molecules. There is ... [more ▼]

Background: High resolution mass spectrometry (HRMS) is being used increasingly in the context of suspect and non-targeted screening for the identification of bioorganic molecules. There is correspondingly increasing awareness that higher confidence identification will require a systematic, group effort to increase the fraction of compounds with tandem mass spectra available in central, publicly available resources. While typical suspect screening efforts will only result in tentative annotations with a moderate level of confidence, library spectral matches will yield higher confidence or even full confirmation of the identity if the reference standards are available. Results: This article first explores representative percent coverage of measured tandem mass spectra in selected major environmental suspect databases of interest in the context of human biomonitoring, demonstrating the current extensive gap between the number of potential substances of interest (up to hundreds of thousands) and measured spectra (0.57–3.6% of the total chemicals have spectral information available). Furthermore, certain datasets are benchmarked, based on previous efforts, to show the extent to which acquired experimental data were comparable between laboratories, even with HRMS instruments based on different technologies (i.e., quadrupole–quadrupole-time of flight versus ion trap/quadrupole-Orbitrap). Instruments and settings that are less comparable are also revealed, primarily linear ion trap instruments, which show distinctly lower comparability. Conclusions: Based on these efforts, harmonization guidelines for the acquisition and processing of tandem mass spectrometry data are proposed to enable European (and ideally worldwide) laboratories to contribute to common resources, without requiring extensive changes to their current in house methods. [less ▲]

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