An Integrated Approach for the Comprehensive Characterization of Metabolites in Broccoli (Brassica oleracea, var. Italica) by Liquid Chromatography High-Resolution Tandem Mass Spectrometry

Background: Broccoli contains diverse phytochemicals, including glucosinolates and their hydrolysis products, with potential nutritional and bioactive properties. Accurate metabolite profiling requires optimized sample preparation and comprehensive databases. Methods: A rapid enzymatic deactivation method with 70% methanol, implemented prior to cryogrinding, was evaluated for processing freeze-dried and fresh broccoli florets, which were compared as plant materials. A widely targeted, organ-resolved metabolite database was constructed by integrating over 612 reported phytochemicals with glucosinolate degradation products. LC-HRMS combined with MS-DIAL and GNPS was employed for metabolite detection and annotation. Results: Freeze-dried samples yielded nearly twice the number of glucosinolates, isothiocyanates, and nitriles compared with standard-processed fresh tissue. Methanol pre-treatment preserved metabolite integrity in fresh samples, achieving comparable sensitivity to freeze-dried material. Using the integrated database, 998 metabolites were identified or tentatively characterized, including amino acids, carboxylic acids, phenolics, alkaloids, terpenoids, and glucosinolate derivatives. Cross-platform reproducibility was improved and false positives reduced. Conclusions: Optimized sample preparation combined with a curated metabolite database enables high-confidence, comprehensive profiling of broccoli florets phytochemicals. The resulting dataset provides a valuable reference for studies on genotype–environment interactions, nutritional quality, and functional bioactivity of cruciferous vegetables.