The principle of the Cooks´kinetic method and its application to analysis of isomeric mixtures are described. The kinetic method based on mass spectrometric measurements is applied to discrimination of isomers of various types of compounds (amino acids, peptides, sugars, pharmaceuticals, etc.). So far this method has been used in static systems (with constant analyte concentrations in the course of analytical run). A modification for dynamic systems (flow injection analysis, HPLC) is presented. The accuracy of determination in both static and dynamic systems can worsen due to different ratios of the isomers in liquid and gas phases. A procedure for correction of this phenomenon is also demonstrated.