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Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples
Corey D Broeckling1, Richard D Beger2, Leo L Cheng3
1Analytical Resources Core: Bioanalysis and Omics Center; Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80525, United States.
Analytical Chemistry
|December 6, 2023
Summary
Pooled quality control (QC) samples are widely used in untargeted metabolomics studies for analytical variance monitoring. However, their application for improving data quality and clear reporting needs significant enhancement across the field.
Area of Science:
- Metabolomics
- Analytical Chemistry
- Biochemistry
Background:
- Untargeted metabolomics is crucial for metabolic phenotyping.
- Data quality assessment in metabolomics is challenging.
- Pooled quality control (QC) samples help monitor analytical variance.
Purpose of the Study:
- To review the use of pooled QC samples in untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics studies.
- To identify current practices, strengths, and deficiencies in pooled QC sample utilization.
- To highlight opportunities for improving data quality reporting and methodology.
Main Methods:
- Scoping literature review of published untargeted LC-MS metabolomics studies.
- Literature query, filtering, and random sampling of articles.
- Review of 109 papers by at least five reviewers using predefined questions.
Main Results:
- Pooled QC samples are widely adopted across different biological taxa and study scales.
- Few studies report using pooled QC samples to actively improve data quality.
- Reporting of QC sample generation and usage methods is often ambiguous or incomplete.
Conclusions:
- There is a significant opportunity to better leverage pooled QC samples for data quality assurance in metabolomics.
- Standardized and detailed reporting of QC sample protocols is needed.
- Enhanced utilization of pooled QC samples can improve the reliability of untargeted LC-MS metabolomics.
