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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 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 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 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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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 & 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 detailTracking complex mixtures of chemicals in our changing environment
Escher, Beate I.; Stapleton, Heather M.; Schymanski, Emma UL

in Science (2020), 367(6476), 388--392

Chemicals have improved our quality of life, but the resulting environmental pollution has the potential to cause detrimental effects on humans and the environment. People and biota are chronically ... [more ▼]

Chemicals have improved our quality of life, but the resulting environmental pollution has the potential to cause detrimental effects on humans and the environment. People and biota are chronically exposed to thousands of chemicals from various environmental sources through multiple pathways. Environmental chemists and toxicologists have moved beyond detecting and quantifying single chemicals to characterizing complex mixtures of chemicals in indoor and outdoor environments and biological matrices. We highlight analytical and bioanalytical approaches to isolating, characterizing, and tracking groups of chemicals of concern in complex matrices. Techniques that combine chemical analysis and bioassays have the potential to facilitate the identification of mixtures of chemicals that pose a combined risk. [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)

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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 detailThe exposome and health: Where chemistry meets biology
Vermeulen, Roel; Schymanski, Emma UL; Barabási, Albert-László et al

in Science (2020), 367(6476), 392--396

Despite extensive evidence showing that exposure to specific chemicals can lead to disease, current research approaches and regulatory policies fail to address the chemical complexity of our world. To ... [more ▼]

Despite extensive evidence showing that exposure to specific chemicals can lead to disease, current research approaches and regulatory policies fail to address the chemical complexity of our world. To safeguard current and future generations from the increasing number of chemicals polluting our environment, a systematic and agnostic approach is needed. The \textquotedblleftexposome\textquotedblright concept strives to capture the diversity and range of exposures to synthetic chemicals, dietary constituents, psychosocial stressors, and physical factors, as well as their corresponding biological responses. Technological advances such as high-resolution mass spectrometry and network science have allowed us to take the first steps toward a comprehensive assessment of the exposome. Given the increased recognition of the dominant role that nongenetic factors play in disease, an effort to characterize the exposome at a scale comparable to that of the human genome is warranted. [less ▲]

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See detailConnecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges
Schymanski, Emma UL; Baker, Nancy C.; Williams, Antony J et al

in Environmental Science. Processes and Impacts (2019)

Connecting chemical exposures over a lifetime to complex chronic diseases with multifactorial causes such as neurodegenerative diseases is an immense challenge requiring a long-term, interdisciplinary ... [more ▼]

Connecting chemical exposures over a lifetime to complex chronic diseases with multifactorial causes such as neurodegenerative diseases is an immense challenge requiring a long-term, interdisciplinary approach. Rapid developments in analytical and data technologies, such as non-target high resolution mass spectrometry (NT-HR-MS), have opened up new possibilities to accomplish this, inconceivable 20 years ago. While NT-HR-MS is being applied to increasingly complex research questions, there are still many unidentified chemicals and uncertainties in linking exposures to human health outcomes and environmental impacts. In this perspective, we explore the possibilities and challenges involved in using cheminformatics and NT-HR-MS to answer complex questions that cross many scientific disciplines, taking the identification of potential (small molecule) neurotoxicants in environmental or biological matrices as a case study. We explore capturing literature knowledge and patient exposure information in a form amenable to high-throughput data mining, and the related cheminformatic challenges. We then briefly cover which sample matrices are available, which method(s) could potentially be used to detect these chemicals in various matrices and what remains beyond the reach of NT-HR-MS. We touch on the potential for biological validation systems to contribute to mechanistic understanding of observations and explore which sampling and data archiving strategies may be required to form an accurate, sustained picture of small molecule signatures on extensive cohorts of patients with chronic neurodegenerative disorders. Finally, we reflect on how NT-HR-MS can support unravelling the contribution of the environment to complex diseases. [less ▲]

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See detailExploring open cheminformatics approaches for categorizing per-and polyfluoroalkyl substances (PFASs)
Sha, Bo; Schymanski, Emma UL; Ruttkies, Christoph et al

in Environmental Science. Processes and Impacts (2019), 21(11), 1835--1851

Per- and polyfluoroalkyl substances (PFASs) are a large and diverse class of chemicals of great interest due to their wide commercial applicability, as well as increasing public concern regarding their ... [more ▼]

Per- and polyfluoroalkyl substances (PFASs) are a large and diverse class of chemicals of great interest due to their wide commercial applicability, as well as increasing public concern regarding their adverse impacts. A common terminology for PFASs was recommended in 2011, including broad categorization and detailed naming for many PFASs with rather simple molecular structures. Recent advancements in chemical analysis have enabled identification of a wide variety of PFASs that are not covered by this common terminology. The resulting inconsistency in categorizing and naming of PFASs is preventing efficient assimilation of reported information. This article explores how a combination of expert knowledge and cheminformatics approaches could help address this challenge in a systematic manner. First, the “splitPFAS” approach was developed to systematically subdivide PFASs (for eventual categorization) following a CnF2n+1–X–R pattern into their various parts, with a particular focus on 4 PFAS categories where X is CO, SO2, CH2 and CH2CH2. Then, the open, ontology-based “ClassyFire” approach was tested for potential applicability to categorizing and naming PFASs using five scenarios of original and simplified structures based on the “splitPFAS” output. This workflow was applied to a set of 770 PFASs from the latest OECD PFAS list. While splitPFAS categorized PFASs as intended, the ClassyFire results were mixed. These results reveal that open cheminformatics approaches have the potential to assist in categorizing PFASs in a consistent manner, while much development is needed for future systematic naming of PFASs. The “splitPFAS” tool and related code are publicly available, and include options to extend this proof-of-concept to encompass further PFASs in the future. [less ▲]

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See detailNon-target screening reveals time trends of polar micropollutants in a riverbank filtration system
Albergamo, Vittorio; Schollée, Jennifer E.; Schymanski, Emma UL et al

in Environmental Science and Technology (2019), 53(13), 7584-7594

The historic emissions of polar micropollutants in a natural drinking water source were investigated by nontarget screening with high-resolution mass spectrometry and open cheminformatics tools. The study ... [more ▼]

The historic emissions of polar micropollutants in a natural drinking water source were investigated by nontarget screening with high-resolution mass spectrometry and open cheminformatics tools. The study area consisted of a riverbank filtration transect fed by the river Lek, a branch of the lower Rhine, and exhibiting up to 60-year travel time. More than 18,000 profiles were detected. Hierarchical clustering revealed that 43% of the 15 most populated clusters were characterized by intensity trends with maxima in the 1990s, reflecting intensified human activities, wastewater treatment plant upgrades and regulation in the Rhine riparian countries. Tentative structure annotation was performed using automated in silico fragmentation. Candidate structures retrieved from ChemSpider were scored based on the fit of the in silico fragments to the experimental tandem mass spectra, similarity to openly accessible accurate mass spectra, associated metadata, and presence in a suspect list. Sixty-seven unique structures (72 over both ionization modes) were tentatively identified, 25 of which were confirmed and included contaminants so far unknown to occur in bank filtrate or in natural waters at all, such as tetramethylsulfamide. This study demonstrates that many classes of hydrophilic organics enter riverbank filtration systems, persisting and migrating for decades if biogeochemical conditions are stable. [less ▲]

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See detailIdentifying Small Molecules in Untargeted Exposomics Data: A case study of Thirdhand Smoke
Schymanski, Emma UL; Torres, Sonia; Ramirez, Noelia

Scientific Conference (2019)

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See detailEnvironmental Cheminformatics to Identify Unknown Chemicals and their Effects
Schymanski, Emma UL

Scientific Conference (2019)

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See detailChemInChIformatics: IUPAC's Role in the Environmental Monitoring Revolution
Schymanski, Emma UL

Scientific Conference (2019)

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See detailMt Sinai Special Seminar: Finding Small Molecules in Big Data
Schymanski, Emma UL

Presentation (2019)

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See detailEstablish data infrastructure to compile and exchange environmental screening data on a European scale
Slobodnik, Jaroslav; Hollender, Juliane; Schulze, Tobias et al

in Environmental Sciences Europe (2019), 31(1), 65

Robust techniques based on liquid (LC) and gas chromatography (GC) coupled with high-resolution mass spectrometry (HR-MS) enable sensitive screening, identification, and (semi)quantification of thousands ... [more ▼]

Robust techniques based on liquid (LC) and gas chromatography (GC) coupled with high-resolution mass spectrometry (HR-MS) enable sensitive screening, identification, and (semi)quantification of thousands of substances in a single sample. Recent progress in computational sciences has enabled archiving and processing of HR-MS ‘big data’ at the routine level. As a result, community-based databases containing thousands of environmental pollutants are rapidly growing and large databases of substances with unique identifiers allowing for inter-comparison at the global scale have become available. A data-archiving infrastructure is proposed, allowing for retrospective screening of HR-MS data, which will help define the ‘chemical universe’ of organic substances and enable prioritisation of toxicants causing adverse environmental effects at the local, river basin, and national and European scale in support of the European water and chemicals management policy. [less ▲]

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