Current practices in LC-MS untargeted metabolomics: a scoping review on the use of pooled quality control samples

Published

December 6, 2023

Author(s)

Clay Davis, Corey Broeckling, Richard Beger, Cheng Leo, Raquel Cumeras, Daniel Cuthbertson, Surendra Dasari, Warwick Dunn, Anne Evans, Álvaro Fernández-Ochoa, Kelli Goodman, Helen Gika, Roy Goodacre, Jennifer Kirwan, Kodra Dritan, Julia Kuligowski, Maria Monge, Jonathan Mosley, Sindhu Nair, Nichole Reisdorph, Stacy Sherrod, Georgios Theodoridis, Candice Ulmer Holland, Dajana Vuckovic, Bo Zhang, Goncalo Gouveia

Abstract

Untargeted metabolomics is an analytical approach with numerous applications, serving as an effective metabolic phenotyping platform to characterize the small molecules within a biological system. Data quality can be challenging to evaluate and demonstrate in untargeted experiments, which has driven the generation and use of a pooled quality control (QC) sample as a valuable approach for untargeted metabolomics, offering the ability to monitor and correct for analytical variance in an untargeted manner. Herein is described a scoping review detailing the use of pooled QC samples in published untargeted liquid chromatography coupled mass spectrometry (LC-MS) based metabolomics studies. The results of the review indicate that the pooled QC sample has been relatively widely adopted by the metabolomics community, that it is used at a similar frequency across biological taxa and sample types, and is used in both small and large studies. However, while many studies generated and analyzed pooled QC samples, the majority did not use the pooled QC sample to improve data quality. There is a clear opportunity for the field to more frequently utilize pooled QC samples for feature filtering, analytical drift correction, and metabolite annotation. Additionally, the adopted survey approach enabled us to assess ambiguity in the methods used to describe the generation and use of pooled QC samples. This analysis indicates that many details of the quality control method are ambiguously written, limiting the reader's ability to determine what quality control steps have been taken. Collectively, these results capture the current state of pooled QC sample usage and highlight strengths and deficiencies in its adoption.

Citation

Analytical Chemistry

Volume

95

Issue

51

Pub Type

Journals

Download Paper

https://doi.org/10.1021/acs.analchem.3c02924

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Keywords

quality control, metabolomics, liquid chromatography coupled mass spectrometry

Citation

Davis, C. , Broeckling, C. , Beger, R. , Leo, C. , Cumeras, R. , Cuthbertson, D. , Dasari, S. , Dunn, W. , Evans, A. , Fernández-Ochoa, Á. , Goodman, K. , Gika, H. , Goodacre, R. , Kirwan, J. , Dritan, K. , Kuligowski, J. , Monge, M. , Mosley, J. , Nair, S. , Reisdorph, N. , Sherrod, S. , Theodoridis, G. , Ulmer Holland, C. , Vuckovic, D. , Zhang, B. and Gouveia, G. (2023), Current practices in LC-MS untargeted metabolomics: a scoping review on the use of pooled quality control samples, Analytical Chemistry, [online], https://doi.org/10.1021/acs.analchem.3c02924, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=936154 (Accessed October 7, 2024)