Novel algorithm for simultaneous component detection and pseudo-molecular ion characterization in liquid chromatography–mass spectrometry

•Novel stepwise component detection algorithm (SCDA) for LC–MS datasets.•New isotopic distribution and adduct-ion models for mass spectra.•Automatic component classification based on adduct-ion and isotopic distributions.

Resolving components and determining their pseudo-molecular ions (PMIs) are crucial steps in identifying complex herbal mixtures by liquid chromatography–mass spectrometry. To tackle such labor-intensive steps, we present here a novel algorithm for simultaneous detection of components and their PMIs. Our method consists of three steps: (1) obtaining a simplified dataset containing only mono-isotopic masses by removal of background noise and isotopic cluster ions based on the isotopic distribution model derived from all the reported natural compounds in dictionary of natural products; (2) stepwise resolving and removing all features of the highest abundant component from current simplified dataset and calculating PMI of each component according to an adduct-ion model, in which all non-fragment ions in a mass spectrum are considered as PMI plus one or several neutral species; (3) visual classification of detected components by principal component analysis (PCA) to exclude possible non-natural compounds (such as pharmaceutical excipients). This algorithm has been successfully applied to a standard mixture and three herbal extract/preparations. It indicated that our algorithm could detect components’ features as a whole and report their PMI with an accuracy of more than 98%. Furthermore, components originated from excipients/contaminants could be easily separated from those natural components in the bi-plots of PCA.

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