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A novel method had been developed for determination of microcystin in surface water by ultra-performance liquid chromatography combined with tandem mass spectrometry (UPLC-MS/MS). Water samples after being concentrated and cleaned with solid phase extraction (SPE) with Oasis HLB cartridge were separated on AcQuity UPLC (TM) BEH C18 column (1.7 mu m, 1.0 x 50 mm) with a gradient elution and a mobile phase consisting of 0.1% formic acid in water and methanol, and then detected with an electrospray ionization tandem mass spectrometry in positive ion mode with multiple reaction monitoring. Compared with traditional liquid chromatography, it took much less time for UPLC to analyze microcystin. Additionally, the UPLC-MS/MS method produced satisfactory reliability, sensitivity, and accuracy. Recoveries of the four microcystins were 91.7-111% with relative standard deviation being 7.9-12%. The calibration curves for microcystins were linear with correlation coefficient being larger than 0.99. Limit of quantification of the four microcystins (microcystin-LR, RR, LW, and LF) after 1000-fold SPE pre-concentration, were 2.5, 6.0, 2.5, and 1.3 ng/L. The presented method had been successfully used to detect microcystin in surface water from the Qiantang River, the West Lake, and three drinking water reservoirs, which represented water bodies of river, lake, and drinking water reservoir, respectively. It was shown that microcystin pollution in drinking water reservoirs was the heaviest, and microcystin-LR and RR were the predominant kinds, with concentrations ranging 0.045-2.73 and 0.021-1.36 mu g/L, respectively. The concentrations of microcystins in river and lake were all under detection limit. (c) 2007 Elsevier Ltd. All rights reserved.