Dataset Information

An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry - Natural Gas Transfer Station GC-HRMS Data

ABSTRACT: This is one of the validation datasets which goes with the manuscript published in Exposome titled an actionable annotation scoring framework for gas chromatography high resolution mass spectrometry. The dataset describes indoor and outdoor air samples collected using passive samplers from homes near natural gas compressor stations.

INSTRUMENT(S): GC Q-Exactive (Thermo)

ORGANISM(S): Na

SUBMITTER: Jonathan Martin Krystal Pollitt

PROVIDER: MSV000090537 | MassIVE | Sat Oct 15 11:16:00 BST 2022

REPOSITORIES: MassIVE

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description: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.

Dataset Information

An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry - Natural Gas Transfer Station GC-HRMS Data

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets