Can we trust biomarkers identified using different non-targeted metabolomics platforms? Multi-platform, inter-laboratory comparative metabolomics profiling of lettuce cultivars via UPLC-QTOF-MS

This study compared the ability of two platforms (Agilent UPLC-ESI-QTOF-MS and Waters UPLC-IMS-QTOF-MS) to identify biomarkers in butterhead and romaine lettuce cultivars.MethodsTwo case studies by different metabolomics platforms: (1) Waters and Agilent datasets processed by the same data pre-processing software (Progenesis QI), and (2) Datasets processed by different data pre-processing software.ResultsA higher number of candidate biomarkers shared between sample groups in case 2 (101) than in case 1 (26) was found. Thirteen metabolites were common to both cases. Romaine lettuce was characterised by phenolic compounds including flavonoids, hydroxycinnamate derivatives, and 9-undecenal, while Butterhead showed sesquiterpene lactones and xanthosine. This study demonstrates that high percentages of the most discriminatory entities can be obtained by using the manufacturers ’ embedded pre-processing software and following the recommended processing data guidelines using commercial software to normalise the data matrix.
Source: Metabolomics - Category: Biology Source Type: research