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Backgrounds   Gentiana rhodantha , a rich source of iridoids and polyphenols, is a traditional ethnomedicine widely used in China. Metabolic fingerprinting based on a LC-UV-MS/MS method was applied to explore the chemical markers for discrimination of  G. rhodantha  from different geographical origins.    Results  Targeted compounds were separated on a Shim-pack XR-ODS III (150 × 2.0 mm, 2.2 μm), with a mobile phase consisted of acetonitrile and 0.1% formic acid in water, under gradient elution. In quantitative analysis, all of the calibration curves showed good linear regression (R 2  < less than 0.9991) within the tested ranges, and accuracy ranged from 97.8% to 104.2% and the %RSD of precision (less than 3%) were all within the required limits. The most abundant mangiferin (82.21 mg/g) found in sample from Zunyi, Guizhou province. Furthermore, 64 samples according to their geographical origins, could be classified by partial least-squares discriminate analysis (PLS-DA) and nine compounds including two new compounds identified by mass spectrometry could be regarded as characteristic compounds for discriminating samples from different geographical origins.    Conclusions  The developed method appears to be a useful tool for analysis of  G. rhodantha , which could provide potential indicators for differentiation of different geographical origins.    Electronic supplementary material  The online version of this article (doi:10.1186/s12858-015-0038-5) contains supplementary material, which is available to authorized users.

Comparative metabolic fingerprinting of Gentiana rhodantha from different geographical origins using LC-UV-MS/MS and multivariate statistical analysis