Growth in the biomedical and biotechnology sectors requires a highly trained and highly skilled workforce to answer the next great scientific questions. Undergraduate laboratory courses incorporating hands-on training based in authentic research position soon-to-be graduates to learn in environments that mirror those of academic, industrial, and government laboratories. Mass spectrometry is one of the most broadly applied analyses carried out in the biomedical and pharmaceutical sciences, and thus, it is essential that upper-division students gain hands-on experience in techniques and analytical workflows in mass spectrometry. Our precourse assessments identified weaknesses in student experience and knowledge in the fundamentals of mass spectrometry, supporting that it was a necessary area for improvement. We incorporated a laboratory experiment focused on tandem mass spectrometry and database searching into a pre-existing mini-semester project devoted to identifying metabolites from medicinal plants. Implementation of the experiment allowed students to make more confident metabolite identifications, introduced them to a cutting-edge database analysis platform (GNPS: Global Natural Products Social Molecular Networking), and increased student experience and knowledge of mass spectrometry in addition to the principle of dereplication of samples derived from nature.