Related Experiment Video
Updated: Jun 29, 2026

Applications of Liquid-Chromatography Tandem Mass Spectrometry in Natural Products Research: Tropane Alkaloids as a Case Study
Published on: March 8, 2024
Decoding MSn fragmentation rules of isoquinoline alkaloids: a comprehensive atlas
Jinqin Ying1, Chunmei Wen1, Yanfang Liu2
1Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China.
None:
Natural products constitute a valuable reservoir of lead compounds for drug discovery. Structural characterization and annotation of isoquinoline alkaloids, an important class of bioactive natural products, are prerequisites for the rapid discovery of novel molecular entities. Interpretation of fragmentation patterns is an indispensable step in structural confirmation of new compounds. However, structurally informative fragmentation behaviors of isoquinoline alkaloids remain insufficiently understood across diverse structural scaffolds. In this study, multistage fragmentation patterns of isoquinoline alkaloids were systematically investigated using high-resolution multistage mass spectrometry (HR-MSn). Through a comprehensive analysis of 139 compounds using HR-MSn, general guidelines and underlying principles were established for the first time. Characteristic skeletal fragmentation pathways, nitrogen-derived group losses, and common neutral losses were systematically elucidated, and several previously unreported fragmentation patterns were identified. In addition, the isomer-dependent fragmentation behavior was investigated. Collectively, these results provide a comprehensive reference framework for the mass spectrometric analysis of isoquinoline alkaloid, thereby laying a solid foundation for future investigations.
Related Concept Videos
Mass Spectrometry: Molecular Fragmentation Overview
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
¹H NMR: Complex Splitting
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
Mass Spectrometry of Amines
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule
Mass Spectrometry: Amine Fragmentation
In amines, the number of nitrogen atoms affects the mass of the molecular ion, which is described by the nitrogen rule of mass spectrometry. This rule states that a compound containing a single or...
Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation
For example, the fragmentation of...
