Multivariate curve resolution based correlation optimized warping (MCR-COW) was proposed as an efficient alignment method to correct the undesirable elution time shifts where co-eluting and shift occurred at the same time and the use of COW algorithm on the raw data often fails. For this purpose, the primary implementation of extended multivariate curve resolution- alternating least squares (MCR-ALS) helped to reduce the underlying complexity of gas chromatography–mass spectrometry (GC–MS) data representing the pure elution and spectral signatures. Afterward, the resolved elution profiles aligned component by component using COW algorithm. Reconstituting of the corrected column wise augmented data was conducted by multiplying of aligned augmented elution profiles with their corresponding spectral profiles to reanalysis by MCR-ALS under optional application of trilinearity constraint. The results obtained from the proposed strategy (MCR-COW-MCR) compared to two common methods MCR-ALS and COW-MCR under application of the same constraints in statistical terms such as lack of fit (LOF), percent of variance explained (R2) under the optimum conditions, concentration and spectral correlation coefficient (R). Also, MCR-BAND method was served to evaluate the extent of rotational ambiguity associated to MCR-ALS and MCR-COW-MCR recovered solutions. Hereby, the presented strategy by improving the accuracy of quantitative and qualitative results provided an opportunity to reach a comprehensive comparative study of the composition and content of volatile constituent's points of view in the peel extract of three varieties of C. aurantium L. named amara, myrtfolia and fasciata. According to the obtained results, considering the oxygenated derivatives of the identified hydrocarbons as an indicator of the high quality of peel extracts and their more high content in amara variety in comparison to other varieties, one can conclude that variety can affect on the amount of oxygenated compounds and
