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A poor repeatability of migration times caused by the fluctuations of electroosmotic flow (EOF) is an inherent weakness of capillary electrophoresis. Most researchers endeavor to prevent this problem using relative migration times or various capillary coatings which are expensive and not easy in comparison. Herein, we present an original approach to this problem: we apply a model sample designed to induce significant EOF instability, in order to critically compare ten capillary types with different physicochemical characteristics. Moreover, we accompany capillary modification with the evaluation of various criteria of peak identification: migration time, migration times ratio, and electrophoretic mobility. Our results show a great effectiveness of a dynamic coating in the stabilization of migration times, with the average RSD(%) value reduced from 3.5% (bare silica capillary) down to 0.5%. The good outcomes were also obtained for the surfactant-modified silica and amine capillaries. For the capillaries exhibiting significant instability of EOF, electrophoretic mobility turned out to be a more universal and reliable criterion of peak identification than relative migration time. It can be explained by an intrinsic dependency of migration times ratio on EOF change, which should always be considered during the selection of an internal standard.Electronic supplementary materialThe online version of this article (doi:10.1007/s00216-017-0382-y) contains supplementary material, which is available to authorized users.

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