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Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples.
Citation:
Broeckling, C., R. Berger, L. Cheng, C. Raquel, D. Cuthbertson, S. Dasari, W. Dunn, A. Evans, A. Fern�ndez-Ochoa, K. Goodman, H. Gika, G. Royston, G. Gouveia, J. Kirwan, D. Kodra, J. Kuligowski, M. Monge, J. Mosley, S. Nair, N. Reisdorph, S. Sherrod, G. Theodoridis, C. Ulmer, D. Vuckovic, AND B. Zhang. Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples. Analytical Chemistry. American Chemical Society, Washington, DC, 95(51):18645–18654, (2023). https://doi.org/10.1021/acs.analchem.3c02924
Impact/Purpose:
Metabolomics approaches are increasingly applied to human health, agriculture, biotechnology, ecology, environmental sciences, toxicology, microbiology, synthetic biology, and regulatory practices. Due to its relatively high sensitivity and broad detection capabilities, liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS or LC-MS) is one of the most widely employed techniques for untargeted metabolomics. However, globally accepted quality management protocols in the field of metabolomics have been slow to develop, in part due to a lack of standardization as it relates to sample type, column chemistry, ionization conditions, mobile phase solvent composition and gradient, among other things. The literature scoping review described herein indicates that the field of untargeted metabolomics has largely embraced pooled quality control samples. However, publication language describing how the pooled QC samples were generated and used is often ambiguous, potentially negatively impacting confidence in the reported results.
Description:
Untargeted metabolomics is an analytical approach with numerous applications serving as an effective metabolic phenotyping platform to characterize small molecules within a biological system. Data quality can be challenging to evaluate and demonstrate in metabolomics experiments. This has driven the use of pooled quality control (QC) samples for monitoring and, if necessary, correcting for analytical variance introduced during sample preparation and data acquisition stages. Described herein is a scoping literature review detailing the use of pooled QC samples in published untargeted liquid chromatography–mass spectrometry (LC-MS) based metabolomics studies. A literature query was performed, the list of papers was filtered, and suitable articles were randomly sampled. In total, 109 papers were each reviewed by at least five reviewers, answering predefined questions surrounding the use of pooled quality control samples. The results of the review indicate that use of pooled QC samples has been relatively widely adopted by the metabolomics community and that it is used at a similar frequency across biological taxa and sample types in both small- and large-scale studies. However, while many studies generated and analyzed pooled QC samples, relatively few reported the use of pooled QC samples to improve data quality. This demonstrates a clear opportunity for the field to more frequently utilize pooled QC samples for quality reporting, feature filtering, analytical drift correction, and metabolite annotation. Additionally, our survey approach enabled us to assess the ambiguity in the reporting of the methods used to describe the generation and use of pooled QC samples. This analysis indicates that many details of the QC framework are missing or unclear, limiting the reader’s ability to determine which QC steps have been taken. Collectively, these results capture the current state of pooled QC sample usage and highlight existing strengths and deficiencies as they are applied in untargeted LC-MS metabolomics.
URLs/Downloads:
DOI: Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples.
https://pubmed.ncbi.nlm.nih.gov/38055671/