An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry

Year: 2022

Type: article

Abstract: 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.

Source: Exposome

DOI: 10.1093/exposome/osac007

Institutions: Yale University, Stockholm University, Science for Life Laboratory, Masaryk University, RECETOX, Brown University, Emory University, Icahn School of Medicine at Mount Sinai, University of Florida, NILU, The FRAM Centre, Örebro University, Columbia University

Language: English

Topic: Metabolomics and Mass Spectrometry Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $2,000

Funders: U.S. Environmental Protection Agency, Yale University, Leona M. and Harry B. Helmsley Charitable Trust, European Commission, Ministerstvo Školství, Mládeže a Tělovýchovy, Svenska Forskningsrådet Formas, Vetenskapsrådet, National Institutes of Health, RECETOX Přírodovědecké Fakulty Masarykovy Univerzity, National Cancer Institute, National Institute of Environmental Health Sciences

OpenAlex ID: W4293051781