We present a mathematical model of CZE based on the concept of eigenmobilities the eigenvalues of matrix M tied to the linearized governing equations of electromigration, and the spectral decomposition of matrix M into matrices of amplitudes P-j. Any peak in an electropherogram, regardless of whether it is an analyte peak or a system peak (system zone), is matched with its matrix P-j. This enables calculation of the peak parameters, such as the transfer ratio and the molar conductivity detection response (which give the indirect detection signal and the conductivity detection signal, respectively), when the initial disturbance caused by the injection of the sample is known. We also introduce new quantities, such as the generalized transfer ratio and the conductivity response of system zones, and show how the amplitude (intensity, area) of the analyte peaks and the system peaks can be calculated. We offer a free software, PeakMaster (http://www.natur.cuni.cz/gas), which yields this information in a user-friendly way.