A generic isocratic HPLC-APCI-MS-MS method has been developed for the determination of plasma concentrations of bioactive compounds for the selection of potential new drug discovery candidates. A 4.6 x 50 mm cyano phase column eluted with an acetonitrile/water mobile phase containing 20 mM ammonium acetate and 0.4% TFA produces retention times of 1 min or less for a wide range of compounds. This is a great advantage in new drug discovery where many compounds are analyzed once and eliminated. No time is consumed developing chromatographic conditions for each new compound. The mass spectrometer can be optimized and the samples can be processed and analyzed, all in the same day. Multiple assays can be run consecutively without changing the column or mobile phase between assays.