A strategy to improve the annotation coverage of small molecule compounds in fruits, vegetables and their products by untargeted metabolomics

Abstract

Metabolomics is essential for analyzing small molecules in food. Effective extraction and separation technology, along with reliable and efficient analytical tools, are essential for enhancing both the quantity and accuracy of compound analysis. Traditional methods relying on single-solvent extraction and single-column separation often result in target omission and reduced annotation coverage. This study presents a 'Divide, Conquer, and Integrate Strategy' for comprehensive untargeted metabolomics in fruits, vegetables, and their products. The method uses three extraction techniques to capture metabolites across a broad polarity range. Each extract is separated using specific chromatographic columns and mobile phases to ensure high annotation coverage. Data are collected via high-resolution mass spectrometry in both positive and negative ion modes, and analyzed using MS-DIAL and MetaboAnalystR. This integrated approach enhances metabolite discovery and annotation accuracy, with low overlap of metabolites annotated by different extraction methods.

Keywords

Untargeted metabolomics / Food / Compound extraction / Annotation analysis / Protocol

Author contributions

The authors confirm contribution to the paper as follows: study conception and design: Yu J, Xu L, Wang K, Xu Z; data collection: Yu J, Zhang N, Zhu X, Mi L, Wang X; analysis and interpretation of results: Yu J, Zhang N, Tang L, Zhu X, Mi L; draft manuscript preparation: Yu J, Xu L, Zhang N, Tang L, Zhu X, Xu Q, Viau C, Xu Z. All authors reviewed the results and approved the final version of the manuscript.

Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Acknowledgments

This research was funded by National Key R&D Program of China (Grant No. 2022YFD2100805).

Conflict of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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