Assess farming production models in tomato crops using a metabolomic approach based on high-resolution mass spectrometry

The lack of reliable chemical markers to distinguish agricultural practices leaves the organic market vulnerable to food fraud. Metabolomic approaches using ultrahigh-performance liquid chromatography coupled with high-resolution-mass-spectrometry (UHPLC-HRMS) and multivariate statistical analysis can identify differences between crops from conventional and organic farming. This approach also helps detect fraudulent organic practices, such as the minimal use of synthetic fertilisers or phytosanitary products, which alter crop metabolism, as shown in this study on tomatoes. The principal component analysis (PCA) of the HRMS compound profiles revealed distinct groups based on the type and amount of fertilisation applied. A negative correlation was observed between the levels of synthetic fertilisers and the abundance of certain markers. Thirteen bioactive compounds, including carotenoids, sterols, and vitamins, were identified as potential markers to differentiate production methods. Taken together, these findings lay an important foundation for differentiating agricultural practices and for developing future classification models to support the integrity of organic products. • The methodology allowed the tentative identification of 13 bioactive compounds. • Seven of them have been reported for the first time in tomato. • The approach differentiated tomatoes grown under different agronomic conditions. • The more fertiliser, the lower the relative abundance of biochemical markers.