Omics-based technologies have enabled comprehensive characterization of our exposure to environmental chemicals (chemical exposome) as well as assessment of the corresponding biological responses at the molecular level (eg, metabolome, lipidome, proteome, and genome). By systematically measuring personal exposures and linking these stimuli to biological perturbations, researchers can determine specific chemical exposures of concern, identify mechanisms and biomarkers of toxicity, and design interventions to reduce exposures. However, further advancement of metabolomics and exposomics approaches is limited by a lack of standardization and approaches for assigning confidence to chemical annotations. While a wealth of chemical data is generated by gas chromatography high-resolution mass spectrometry (GC-HRMS), incorporating GC-HRMS data into an annotation framework and communicating confidence in these assignments is challenging. It is essential to be able to compare chemical data for exposomics studies across platforms to build upon prior knowledge and advance the technology. Here, we discuss the major pieces of evidence provided by common GC-HRMS workflows, including retention time and retention index, electron ionization, positive chemical ionization, electron capture negative ionization, and atmospheric pressure chemical ionization spectral matching, molecular ion, accurate mass, isotopic patterns, database occurrence, and occurrence in blanks. We then provide a qualitative framework for incorporating these various lines of evidence for communicating confidence in GC-HRMS data by adapting the Schymanski scoring schema developed for reporting confidence levels by liquid chromatography HRMS (LC-HRMS). Validation of our framework is presented using standards spiked in plasma, and confident annotations in outdoor and indoor air samples, showing a false-positive rate of 12% for suspect screening for chemical identifications assigned as Level 2 (when structurally similar isomers are not considered false positives). This framework is easily adaptable to various workflows and provides a concise means to communicate confidence in annotations. Further validation, refinements, and adoption of this framework will ideally lead to harmonization across the field, helping to improve the quality and interpretability of compound annotations obtained in GC-HRMS.

Department of Chemistry University of Florida Gainesville FL USA

Department of Environmental Health Science Yale School of Public Health New Haven CT USA

Department of Environmental Science Science for Life Laboratory Stockholm University Stockholm Sweden

Department of Physiological Sciences Center for Environmental and Human Toxicology University of Florida Gainesville FL USA

Icahn School of Medicine at Mount Sinai Department of Environmental Medicine and Public Health New York NY USA

Mailman School of Public Health Department of Environmental Health Sciences Columbia University New York NY USA

MTM Research Centre Örebro University Örebro Sweden

National Facility for Exposomics Metabolomics Platform Science for Life Laboratory Stockholm University Solna 171 65 Sweden

NILU Norwegian Institute for Air Research Framsenteret Tromsø Norway

NILU Norwegian Institute for Air Research Kjeller Norway

RECETOX Faculty of Science Masaryk University Kotlarska 2 Brno Czech Republic

School of Engineering Brown University Providence RI USA

School of Medicine Department of Medicine Emory University Atlanta GA USA

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High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage