Amine metabolites play crucial roles in biological systems and serve as biomarkersfor various diseases. In this study, we developed a cost-effective derivatizationmethod based on N-tert-butyloxycarbonylation (Boc), which is themost affordable among previously reported amine derivatization methods. Thisenvironmentally friendly approach enhances the retention and detection ofamine metabolites in reversed-phase liquid chromatography-mass spectrometry,with Boc derivatives demonstrating excellent stability for at least 20 days at4C and 60 days at 20C. Importantly, Boc derivatization does not affect thesignal intensity or the number of non-amine metabolites, ensuring themethod’s compatibility with untargeted metabolomics workflows. The effectivenessof this method was validated using immature rice seed extracts fromjaponica and indica cultivars. Boc derivatization enabled the signal detection of54 amine metabolites, with comparative analysis identifying 11 significantly differentiatedmetabolites between the two rice varieties, including histidine,methionine, pipecolate, and GABA. The specificity and robustness of thismethod confirm its utility for discovering biologically relevant metabolites incomplex biological and agricultural samples. With its simplicity, catalyst-freeworkflow, stability, and improved sensitivity, the Boc derivatization methodrepresents a valuable tool for amine metabolite screening in metabolomicsresearch, offering a cost-effective and efficient solution for untargeted analysis.