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

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.