Data Fusion Combining High-Resolution Mass Spectrometry and 1H-NMR Metabolomic Data with Gluten Protein Content to Assess the Impact of Agro-Sustainable Treatments on Durum Wheat

Sustainable food production systems based on the use of biofertilizers and soil improvers are proposed to mitigate agricultural-related environmental impacts and address the climate crisis. In particular, plant growth-promoting microbes (PGPM) and biochar (Char) have been reported to improve plant growth, soil quality, and crop yield; however, their effects on food quality remain debated. In this study, untargeted metabolomics based on ultra-high performance liquid chromatography–ion mobility–high-resolution mass spectrometry (UHPLC-IMS-HRMS) and proton nuclear magnetic resonance spectroscopy (1H-NMR) are proposed to achieve a comprehensive investigation of the effects of Char, PGPM and Char+PGPM on durum wheat. A total of 88 metabolites were annotated by UHPLC-IMS-HRMS, mainly belonging to carbohydrates, flavones, flavonoids, glycerophospholipids, and glycolipids, while 30 compounds were annotated by 1H-NMR, mostly amino acids and short-chain carboxylic acids. The two datasets were merged with the gluten protein content dataset by using low- and mid-level data fusion approaches, obtaining models that exhibit excellent classification performance. Integrated analysis highlighted that the combined Char+PGPM treatment induced metabolic changes across multiple chemical classes, including enrichment of flavonoids and lipids, and downregulation of carbohydrate metabolites, suggesting a redistribution of carbon resources and modulation of secondary metabolism with potential implications on wheat grain quality.