A method and apparatus for controlling fraction collection in an eluent stream flowing from an LC column. A triggering detector recognizes the presence of a target substance according to characteristics of chromatographic peaks in the eluent stream and initiates a delay timer to trigger the fraction collector. A waste stream detector is disposed at any distance from the fraction collector to detect peaks in the waste stream flowing from a fraction collector. The signature of fraction collector actuation is seen by the waste stream detector, permitting the delay time to be adjusted for optimal collection of the target compound. The presence or absence of a peak or the characteristics of a remnant peak detected by the waste stream detector are used to confirm that the target component of the eluent stream was collected as intended by the fraction collector.