Advanced LC-MS/MS methodologies for the analysis of neuroactive compounds in tomato-based diets: Insights from 2D In Vitro digestion models

• LC–MS methods developed for 41 neuroactive compounds in fresh/digested tomato and fecal samples. • In vitro digestion showed diverse compound behaviours. • Fecal fermentation revealed selective microbial transformations and resistance. • Neuro-disrupting compounds resisted microbiome-driven transformation. • New insights into the fate of neuroactive compounds once digested. The digestive fate of neuroactive food compounds remains poorly understood despite growing interest in their role in brain health. This study developed advanced analytical methods to identify neuroprotective and neuro-disrupting compounds in tomatoes before and after digestion and following fecal fermentation. Using in vitro digestion and fermentation models, we characterized compound behavior during digestion. Most compounds were quantified in undigested tomatoes. Digestion revealed diverse outcomes: some compounds transformed (e.g., chlorogenic acids), others produced (e.g., linoleic acid), and several remained stable with potential to reach the colon (e.g., serotonin, rutin). Notably, neuro-disrupting compounds like bisphenols remained largely unaltered and bioaccessible in the colon. Fecal fermentation further showed dynamic changes, with some compounds decreasing (e.g., rutin) and others increasing (e.g., quercetin). These findings provide both methodological advances and mechanistic insights into neuroactive compound behavior during digestion, informing future research on gut-mediated dietary effects in the context of neurodegenerative disease prevention.