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

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. Systematically measuring exposures and linking these stimuli to biological perturbations can determine specific chemical exposures of concern, mechanisms and biomarkers of toxicity, and interventions. However, advancement of exposomics is limited by a lack of harmonization of gas chromatography high-resolution mass spectrometry (GC-HRMS) methods used for data acquisition and approaches for assigning confidence to chemical annotations. Here we discuss the major pieces of evidence provided by 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 high-resolution mass spectrometry (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.

Suspect Screening Analysis of Pooled Human Serum Samples Using GC × GC/TOF-MS

“…50 A total of 544 substances were identified across 16 serum pools. Eleven substances were confirmed with analytic standards (Level 1 Identification) 38 in the pooled samples, while only five substances were confirmed in the SRM (confirmed substances are shown in Supporting Information Figure 3; all chemicals that underwent targeted confirmation are provided in Supporting Information Table 1). There were 174 unique substances tentatively identified (Level 2 Identification) through either basic processing (61 unique substances) or CPR processing (117 unique substances).…”

“…Chemical Identification and Confidence Level Assignment. Tentative chemical identifications were assigned using the confidence levels proposed by Koelmel et al 38 Levels reported here are Level 1, a confirmed identification made using a chemical standard; Level 2, a probable structure assigned based on favorable matching between experimental MS/MS spectrum and the National Institute of Standards and Technology 2014 Mass Spectral library, version 2.2.07�2014 (NIST 2014); and Level 3, tentative isomer identification where the spectra are similar, but the exact isomer, carbon chain length, or location of functional groups on the carbon chain of a substance is not certain. Further explanations of the types of identifications used in this study can be found in the Supporting Information.…”

Disposable Polypropylene Face Masks: A Potential Source of Micro/Nanoparticles and Organic Contaminates in Humans

“… a DF refers to the detection frequency in all 20 brands of masks. b CL refers to the structural confidence level of tentatively identified organic compounds according to the criteria of Koelmel et al A CL of 1 means the chemical has been confirmed vs an analytical standard. A CL of 2 means the chemical could also be other isomers of the same core structure.…”

“…Full scan spectral data were deconvoluted into different feature groups (i.e., a group of mass spectral peaks of the same retention time and highly similar peak shapes) and matched to the NIST spectral library (version 2017, National Institute of Standards and Technology). The most probable candidate for each feature group was obtained by filtering key matching parameters (e.g., "score", "SI", and "ΔRI") according to the rules detailed in the Supporting Information, and a confidence level (CL) was assigned to each tentatively identified chemical according to the criteria described by Koelmel et al 36 In addition, for each brand, only chemicals detected in all three masks were reported. For all tentatively identified chemicals, the internal standard corrected peak areas were calculated, and for some of the chemicals with higher values, candidate standards were procured for structural confirmation and quantification.…”

Heterogeneous Photodegradation Behavior of Liquid Crystal Monomers in Dust: Quantitative Structure–Activity Relationship and Product Identification

“…Compounds with delta RI less than 20 were deemed reliable. 49 LC-HRMS analysis was conducted using a UHPLC-Orbitrap system (Ultimate 3000/Orbitrap Fusion, Thermo Fisher Scientific) equipped with a UPLC BEH C18 column (50 mm × 2.1 mm × 1.7 μm, Thermo Fisher Scientific). Positive and negative electrospray ionization modes were performed separately.…”