Matrix interferents are removed from pharmaceutical samples via an on-line, automated column switching process in which the difference in hydrophobicity between the analyte and the interferents allows these species to be isolated in different parts of the chromatographic system. In this case, the interferents are trapped on a cleanup column and are flushed to waste as the analyte undergoes additional separation on an analytical column. The utility of this approach is demonstrated by the quantitation of citrate in pharmaceutical samples by ion suppression, reversed-phase liquid chromatography. The performance of this system is statistically equivalent to that of a manual pretreatment method employing disposable, solid-phase extraction cartridges.