RationaleAlthough it is claimed that desorption electrospray ionization (DESI) causes less ion suppression effects than electrospray ionization (ESI), a related investigation with quantification measurement of ion suppression effects is absent. Herein, a comparative analysis of ion suppression effects between DESI and ESI was conducted, with the aiming of quantitatively studying the ion suppression effect.MethodsCTVA mixtures, a constant concentration of tioconazole with varied concentrations of atenolol, were analyzed by ESI and DESI. The ion suppression effect was characterized by the signal loss of tioconazole in the mixture compared to the signal intensity of tioconazole without interference (denoted as (Isingle − Imixture)/Isingle). According to the variations in the experimental conditions (such as flow rate, solvent composition, substrate material, capillary inner diameter, sheath gas velocity), ion suppression effects in DESI and ESI were compared.ResultsWith the increasing flow rate, the ion suppression effect in DESI became weaker, while the opposite trend was obtained for ESI. As for capillary inner diameter, a smaller inner diameter resulted in weaker ion suppression effects in DESI and ESI. The solvent composition affected the ion suppression effect, and the PTFE substrate presented the weakest ion suppression effect among the five substrate materials.ConclusionsThough the ion suppression effect in DESI and ESI was shown to relate to experimental conditions, DESI had less effect than ESI under the same experimental conditions in most cases. Moreover, DESI displayed stronger matrix‐tolerant ability than ESI which is also attributed to the weaker ion suppression effect.