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Background  Karrikins (KARs) are recently described group of plant growth regulators with stimulatory effects on seed germination, seedling growth and crop productivity. So far, an analytical method for the simultaneous targeted profiling of KARs in plant tissues has not been reported.    Results  We present a sensitive method for the determination of two highly biologically active karrikins (KAR 1  and KAR 2 ) in minute amounts of plant material (< 20 mg fresh weight). The developed protocol combines the optimized extraction and efficient single-step sample purification with ultra-high performance liquid chromatography-tandem mass spectrometry. Newly synthesized deuterium labelled KAR 1  was employed as an internal standard for the validation of KAR quantification using a stable isotope dilution method. The application of the matrix-matched calibration series in combination with the internal standard method yields a high level of accuracy and precision in triplicate, on average bias 3.3% and 2.9% RSD, respectively. The applicability of this analytical approach was confirmed by the successful analysis of karrikins in  Arabidopsis  seedlings grown on media supplemented with different concentrations of KAR 1  and KAR 2  (0.1, 1.0 and 10.0 µmol/l).    Conclusions  Our results demonstrate the usage of methodology for routine analyses and for monitoring KARs in complex biological matrices. The proposed method will lead to better understanding of the roles of KARs in plant growth and development.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13007-021-00738-1.

A stable isotope dilution method for a highly accurate analysis of karrikins