Abstract <p>Drift ion mobility spectrometry (DIMS) is a well-recognized method for studying the structure of matter. It is widely used for the identification of narcotic and explosive substances, as well as in biomedical research as part of hybrid mass-spectrometric techniques. An experimental method based on signal multiplexing with the Hadamard transform has a significant impact on the quality of the data obtained. However, artifacts in the decoded multiplexed signal remain a major obstacle to the expansion of this method. A number of scientific groups have proposed a variety of approaches to suppress artifacts, but the reasons for the artifact formation remain controversial. Along with the search for and development of applied methods for reducing the effect of artifacts, the authors consider it advisable to develop a theoretical basis for the appearance of modulation errors, which will ensure a mathematically correct elimination of these errors from the results of Hadamard transformations. In this work, using an ion mobility spectrometer with a Faraday plate detector, we investigated possible reasons for the systematic signal modulation error. The two proposed reasons include the Coulomb repulsion of ion packets and the heterogeneity of the contributions of individual sections of pseudorandom sequences. We also described a mathematical procedure for artifact formation, which takes into account the effect of the second reason. A comparison of mathematically calculated artifacts with the experimentally observed ones was done for a statistically significant number of modulating sequences, on the basis of which we concluded that the heterogeneity of the contributions of individual sections of pseudo-random sequences has a predominant effect.</p>