PubChemLite Plus Collision Cross Section (CCS) Values for Enhanced Interpretation of Nontarget Environmental Data

Environmental Science & Technology Letters, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Finding relevant chemicals in the vast (known) chemical space is a major challenge for environmental and exposomics studies leveraging nontarget high resolution mass spectrometry (NT-HRMS) methods. Chemical databases now contain hundreds of millions chemicals, yet many are not relevant. This article details an extensive collaborative, open science effort to provide dynamic collection environmental, metabolomics, research, along with supporting information about their relevance assist researchers interpretation candidate hits. The PubChemLite Exposomics compiled from ten annotation categories within PubChem, enhanced patent, literature counts, predicted partition coefficient (logP) values, as well collision cross section (CCS) values using CCSbase. Monthly versions archived on Zenodo under CC-BY license, reproducible new interface has been developed, including historical trends patent data, browse collection. how can support studies, describes efforts increase availability experimental CCS explores known limitations potential future developments. data code behind these openly available. be browsed at https://pubchemlite.lcsb.uni.lu.

Language: Английский

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From Complexity to Clarity: Expanding Metabolome Coverage With Innovative Analytical Strategies

Journal of Separation Science, Journal Year: 2025, Volume and Issue: 48(2)

Published: Feb. 1, 2025

ABSTRACT Metabolomics, a powerful discipline within systems biology, aims at comprehensive profiling of small molecules in biological samples. The challenges sample complexity are addressed through innovative preparation methods, including solid‐phase extraction and microextraction techniques, enhancing the detection quantification low‐abundance metabolites. Advances chromatographic separation, particularly liquid chromatography (LC) gas (GC), coupled with high‐resolution (HR) mass spectrometry (MS), have significantly improved sensitivity, selectivity, throughput metabolomic studies. Cutting‐edge such as ion‐mobility (IM‐MS) tandem MS (MS/MS), further expand capacity for metabolite profiling. These advanced analytical platforms each offer unique advantages metabolomics, continued technological improvements driving deeper insights into metabolic pathways biomarker discovery. By providing detailed overview current trends this review to valuable future metabolomics human health research its translational potential clinical settings. Toward end, also highlights biomedical applications emphasizing role discovery, disease diagnostics, personalized medicine, drug development.

Language: Английский

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Liquid and gas-chromatography-mass spectrometry methods for exposome analysis

Journal of Chromatography A, Journal Year: 2025, Volume and Issue: unknown, P. 465728 - 465728

Published: Jan. 1, 2025

Language: Английский

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The Exposome and Human Health

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: 59(2), P. 991 - 992

Published: Jan. 21, 2025

InfoMetricsFiguresRef. Environmental Science & TechnologyVol 59/Issue 2Article This publication is free to access through this site. Learn More CiteCitationCitation and abstractCitation referencesMore citation options ShareShare onFacebookX (Twitter)WeChatLinkedInRedditEmailJump toExpandCollapse EditorialJanuary 21, 2025The Exposome Human HealthClick copy article linkArticle link copied!Pablo Gago-Ferrero*Pablo Gago-FerreroInstitute of Assessment Water Research, IDAEA-CSIC, 08034 Barcelona, Spain*[email protected]More by Pablo Gago-Ferrerohttps://orcid.org/0000-0002-5987-0399Ian CousinsIan CousinsStockholm University, Stockholm 114 19, SwedenMore Ian Cousinshttps://orcid.org/0000-0002-7035-8660Akhgar GhassabianAkhgar GhassabianNYU Langone Health, New York, York 10016, United StatesMore Akhgar Ghassabianhttps://orcid.org/0000-0001-9551-4706Marja LamoreeMarja LamoreeVrije Universiteit Amsterdam, 1081 HV The NetherlandsMore Marja LamoreeDaniel SchlenkDaniel SchlenkUniversity California, Riverside, California 92521, Daniel SchlenkLeisa-Maree TomsLeisa-Maree TomsQueensland University Technology (QUT), Brisbane 4000, AustraliaMore Leisa-Maree Tomshttps://orcid.org/0000-0002-1444-1638Bin WangBin WangPeking Beijing 100871, ChinaMore Bin Wanghttps://orcid.org/0000-0002-1164-8430Julie ZimmermanJulie ZimmermanYale Haven, Connecticut 06520, Julie Zimmermanhttps://orcid.org/0000-0002-5392-312XOpen PDFEnvironmental TechnologyCite this: Environ. Sci. Technol. 2025, 59, 2, 991–992Click citationCitation copied!https://pubs.acs.org/doi/10.1021/acs.est.4c13478https://doi.org/10.1021/acs.est.4c13478Published January 2025 Publication History Received 3 December 2024Published online 21 2025Published in issue 2025editorialCopyright © Published American Chemical Society. available under these Terms Use. Request reuse permissionsThis licensed for personal use ACS PublicationsCopyright SocietySubjectswhat are subjectsArticle subjects automatically applied from the Subject Taxonomy describe scientific concepts themes article.BacteriaEnvironmental pollutionEnvironmental scienceImpuritiesMixturesIt now well understood that an individual's unique characteristics arise intricate interaction between genes a vast range nongenetic factors. While only small fraction diseases can be solely attributable genetics, studies factors have been sporadic mostly focused on single factor or limited To address imbalance, concept exposome has emerged, offering broader perspective human health. represents comprehensive collection all physical, chemical, biological, psychosocial which individuals exposed conception onward, along with their internal biological responses, collectively shape health outcomes. (1) Because remarkable advances measurement techniques analytical methods, become increasingly prominent environmental biomedical research. paradigm shift enabled identification causal relationships specific For example, exposure certain chemical mixtures, whether voluntary involuntary, linked onset various metabolic disorders. (2) Notably, recent exposome-wide association (EWAS) aging mortality within UK Biobank, encompassing nearly half million participants, demonstrated all-cause influenced more than genome. (3) Despite advancements, studying remains highly complex. Its dynamic nature, wide diversity exposures, continuous variation over lifetime present significant challenges. fully comprehend exposome's impact health, multidisciplinary approach essential. Integration expertise diverse fields, such as chemistry, toxicology, epidemiology, science engineering, clinical medicine, omic data science, etc., necessary. Such framework key unraveling connections exposures As we advance frontiers research, provides critical pathway understanding disease etiology, fostering personalized preventive healthcare strategies, holistic view profound links environment health.Research still its early stages, presenting opportunities due advancements technology but also raising questions. (ES&T) aims remain at forefront field. Seminal published journal expanded our faced mechanisms linking diseases. new Special Issue, "The Health", brings together 77 outstanding manuscripts, including 68 research papers, four perspectives, one viewpoint, reviews, delve into array topics exposomic transdisciplinary field dedicated discovery-based how influences biology (4) These contributions offer insights mapping (defined chemicals may exposed) using state-of-the-art mass spectrometry techniques, both important legacy emerging contaminants, endocrine disruptors, persistent organic pollutants, toxic metals, microplastics, relying statistical approaches handling mixture exposure, biomarkers profiling assess individual population-level wearables assessment, innovative outcomes vitro vivo models, (5) integration multiomics technologies unravel molecular disease.It worth highlighting extensive review coordinated G. Miller 45 co-authors, surveys literature high-resolution offers up-to-date primer chemists, toxicologists, epidemiologists, providers, other stakeholders. serves reference point current state Additionally, many articles emphasize methodological characterizing implications vulnerable populations, particularly pregnant young children, long-term effects complex mixtures. A notable theme across manuscripts growing recognition importance holistic, integrated exposures. From assessing role contaminants altering semen quality exploring perturbations per- polyfluoroalkyl substances examining traffic changes gut microbiome, papers highlight need consider full spectrum biotic abiotic, interactions genetic, metabolic, lifestyle By advancing special inform public interventions regulatory policies aimed mitigating risks posed contaminants.As editors extend heartfelt thanks authors insightful reviewers efforts constructive feedback. inspire community encourage development will continue push boundaries It collaborative effort hope build healthier, sustainable future, addressing challenges are, paradoxically, often too restrained ensure population.Author InformationClick section linkSection copied!Corresponding AuthorPablo Gago-Ferrero, Associate Editor ES&T, Institute Spain, https://orcid.org/0000-0002-5987-0399, Email: [email protected]AuthorsIan Cousins, Sweden, https://orcid.org/0000-0002-7035-8660Akhgar Ghassabian, Guest Editor, NYU States, https://orcid.org/0000-0001-9551-4706Marja Lamoree, Vrije NetherlandsDaniel Schlenk, Executive ES&T Letters, StatesLeisa-Maree Toms, Queensland Australia, https://orcid.org/0000-0002-1444-1638Bin Wang, Peking China, https://orcid.org/0000-0002-1164-8430Julie Zimmerman, Editor-in-Chief Yale https://orcid.org/0000-0002-5392-312XReferencesClick copied! references 4 publications. 1Wild, C. P. Complementing genome ″exposome″: challenge epidemiology. Cancer Epidemiol. Biomarkers 2005, 14 (8), 1847– 1850, DOI: 10.1158/1055-9965.EPI-05-0456 Google ScholarThere no corresponding record reference.2Vuong, A. M.; Yolton, K.; Braun, J. Lanphear, B. P.; Chen, mixtures neurobehavior: epidemiologic findings future directions. Reviews Health 2020, 35 (3), 245– 256, 10.1515/reveh-2020-0010 reference.3Argentieri, M. A.; Amin, N.; Nevado-Holgado, J.; Sproviero, W.; Collister, Keestra, S. Doherty, Hunter, D. Alvergne, Duijn, v. Integrating genetic architectures aging. medRxiv 2023, 10.1101/2023.03.10.23286340 reference.4Lai, Y.; Koelmel, Walker, I.; Price, E. Papazian, S.; Manz, K. E.; Castilla-Fernández, D.; Bowden, Nikiforov, V.; David, Bessonneau, Amer, B.; Seethapathy, Hu, X.; Lin, Z.; Jbebli, McNeil, R.; Barupal, Cerasa, Xie, H.; Kalia, Nandakumar, Singh, Tian, Gao, Zhao, Froment, Rostkowski, Dubey, Coufalíková, Seličová, Hecht, Liu, Udhani, H. Restituito, Tchou-Wong, K.-M.; Lu, Martin, Warth, Godri Pollitt, Klánová, Fiehn, O.; Metz, T. Pennell, Jones, Miller, W. High-Resolution Mass Spectrometry Exposomics: Expanding Space Coverage. 2024, 58, 12784– 12822, 10.1021/acs.est.4c01156 reference.Cited Click copied!This not yet cited publications.Download PDFFiguresReferences Get e-AlertsGet e-AlertsEnvironmental copied!https://doi.org/10.1021/acs.est.4c13478Published 2025Copyright permissionsArticle Views-Altmetric-Citations-Learn about metrics closeArticle Views COUNTER-compliant sum text downloads since November 2008 (both PDF HTML) institutions individuals. regularly updated reflect usage leading up last few days.Citations number citing article, calculated Crossref daily. Find information counts.The Altmetric Attention Score quantitative measure attention received online. Clicking donut icon load page altmetric.com additional details score social media presence given article. calculated.Recommended Articles FiguresReferencesThis figures.References There reference.

Language: Английский

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The role of residual (veterinary) antibiotics in chemical exposome analysis: Current progress and future perspectives

Comprehensive Reviews in Food Science and Food Safety, Journal Year: 2025, Volume and Issue: 24(2)

Published: Feb. 4, 2025

Abstract Humans are exposed to a complex mixture of environmental and food‐related chemicals throughout their lifetime. Exposome research intends explore the nongenetic, that is, causes chronic disease interactions comprehensively. Residual antibiotics can enter human body through therapeutics, foods animal origin, aquatic products, or drinking water. In last decade, significant levels residual in urine have been described, demonstrating frequent exposure populations. To which extent they contribute health risks is debated. Human biomonitoring (HBM) aims determine quantify concentrations xenobiotics specimens provides toolbox monitor diverse chemical exposures. Due public implications, priority‐listed routinely monitored European Union other countries. However, antibiotics, an important class (food‐derived) xenobiotics, still not systematically investigated for better more holistic understanding context exposomics. This review comprehensive summary HBM related existing liquid chromatography–mass spectrometry (LC–MS)‐based analytical methods, potential caused by unintended exposure. Incorporating into exposome framework routine using multiclass methods will provide toxicological pharmacological effects and, ultimately, exposome.

Language: Английский

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An Enhanced Protocol to Expand Human Exposome and Machine Learning-Based Prediction for Methodology Application

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 10, 2025

The human exposome remains limited due to the challenging analytical strategies used reveal low-level endocrine-disrupting chemicals (EDCs) and their metabolites in serum urine. This limits integrity of EDC exposure assessment hinders understanding cumulative health effects. In this study, we propose an enhanced protocol based on multi-solid-phase extraction (multi-SPE) expand with polar EDCs train a machine learning (ML) model for methodology prediction molecular descriptors. measurement 70 (25%) 34 (12%) out 295 well-acknowledged urine compared hydrophilic–lipophilic balance sorbent alone. nontarget analysis from 20 women childbearing age cohort 498, controlling occupational factors daily behaviors high chemical potential, multi-SPE increased 10 (40%) 16 (53%) target identification 17 (77%) (36%) (confidence ≥ level 3) urine, respectively. Interestingly, ML predicted that could identify additional 38% most bioactive chemicals. conclusion, advances by expanding profiles.

Language: Английский

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Novel Method for Simultaneously Untargeted Metabolome and Targeted Exposome Analysis in One Injection

Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 12, 2025

Serum endogenous metabolites and coexisting exogenous compounds are closely related to human health. Metabolomics often uses high-resolution mass spectrometry (HRMS), but current exposomics studies typically rely on triple quadrupole tandem due lower concentrations in the body. As a result, metabolome-exposome-wide association (mEWAS) require combination of untargeted metabolomics several targeted methods measure more exposures, leading increased time sample consumption. In this study, novel method was proposed by leveraging advantages recently introduced Zeno MRMHR technology; it allows for simultaneous acquisition metabolome HRMS exposome multiple reaction monitoring (MRM) modes one injection. The signal responses MRM were comparable those HRMS. This rigorously validated, all standards had relative standard deviations (RSDs) below 20% intraday interday repeatability. Over 90% metabolic features exhibited RSDs these assessments. also broad quantification range, with limits (LLOQ) from 0.1 25 ng/mL higher (HLOQ) 2.5 1000 ng/mL. approach demonstratively applied type 2 diabetes mellitus cohort identify serum risk factors study metabolome-exposome association. To our knowledge, is first implementation unified analysis mode 210 injection, offering tool mEWAS research.

Language: Английский

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Exposome Burden Scores to Summarize Environmental Chemical Mixtures: Creating a Fair and Common Scale for Cross-study Harmonization, Report-back and Precision Environmental Health

Current Environmental Health Reports, Journal Year: 2025, Volume and Issue: 12(1)

Published: Feb. 18, 2025

Language: Английский

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Reference Library for Suspect Non-targeted Screening of Environmental Toxicants Using Ion Mobility Spectrometry-Mass Spectrometry

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

As our health is affected by the xenobiotic chemicals we are exposed to, it important to rapidly assess these molecules both in environment and bodies. Targeted analytical methods coupling either gas or liquid chromatography with mass spectrometry (GC-MS LC-MS) commonly utilized current exposure assessments. While accepted as gold standard for analyses, they often require multiple sample preparation steps more than 30 minutes per sample. This throughput limitation a critical gap assessments has resulted an evolving interest using ion mobility MS (IMS-MS) non-targeted studies. IMS-MS unique technique due its rapid capabilities (millisecond scanning) detection of wide range based on collision cross section (CCS) mass-to-charge ( m/z ) values. To increase availability information studies, here drift tube evaluate 4,685 chemical standards from Environmental Protection Agency Toxicity Forecaster (ToxCast) program including pesticides, industrial chemicals, pharmaceuticals, consumer products, per- polyfluoroalkyl substances (PFAS). In 3,993 [M+H] + , [M+Na] [M-H] - [M+] types were observed high confidence reproducibility (≤1% error intra-laboratory ≤2% inter-laboratory) 2,140 chemicals. These values then assembled into openly available multidimensional database uploaded PubChem enable suspect screening environmental contaminants, faster response time assessments, xenobiotic-disease connections.

Language: Английский

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Global research trends on the human exposome: a bibliometric analysis (2005–2024)

Environmental Science and Pollution Research, Journal Year: 2025, Volume and Issue: unknown

Published: March 8, 2025

Abstract Exposome represents one of the most pressing issues in environmental science research field. However, a comprehensive summary worldwide human exposome is lacking. We aimed to explore bibliometric characteristics scientific publications on exposome. A analysis from 2005 December 2024 was conducted using Web Science accordance with PRISMA guidelines. Trends/hotspots were investigated keyword frequency, co-occurrence, and thematic map. Sex disparities terms citations examined. From 2024, 931 published 363 journals written by 4529 authors 72 countries. The number tripled during last 5 years. Publications females (51% as first 34% authors) cited fewer times (13,674) than males (22,361). Human studies mainly focused air pollution, metabolomics, chemicals (e.g., per- polyfluoroalkyl substances (PFAS), endocrine-disrupting chemicals, pesticides), early-life exposure, biomarkers, microbiome, omics, cancer, reproductive disorders. Social built environment factors, occupational multi-exposure, digital exposure screen use), climate change, late-life received less attention. Our results uncovered high-impact countries, institutions, journals, references, authors, key trends/hotspots. use technologies sensors, wearables) data artificial intelligence) has blossomed overcome challenges could provide valuable knowledge toward precision prevention. risk scores represent promising avenue.

Language: Английский

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