Widespread occurrence of in‐source fragmentation in the analysis of natural compounds by liquid chromatography–electrospray ionization mass spectrometry

RATIONALE: The in-source fragmentation (ISF) of analyte or co-eluting substances produces unintentional fragment ions, which hampers identification and quantification by liquid chromatography-mass spectrometry (LC/MS). Natural compounds derived from plants also contain fragile moieties that may undergo ISF. However, the characteristics of ISF of natural compounds in LC/MS are still unclear. METHODS: The ISF behavior of 214 natural compounds was assayed in LC with Q/orbitrap MS in electrospray ionization (ESI) mode and the extent of ISF was evaluated. RESULTS: fragmentation patterns with precursor ions of the homologs in plants. Furthermore, severe ISF may cause a false negative in the identification of the parent form. CONCLUSIONS: In summary, ISF was a highly frequent phenomenon for analysis of natural compounds by LC/ESI-MS, and extensive and successive ISF of natural products may cause misannotation and misidentification with homologs in plants. The study should raise awareness of ISF interference during the analysis of natural compounds.