A plurality of MRM transitions to be used to monitor a sample are received and divided into two or more contiguous groups. At least one sentinel transition is selected in each group that identifies a next group of the two or more contiguous groups that is to be monitored. A first group of the two or more contiguous groups is placed on a duty cycle list of the tandem mass spectrometer. One or more compounds are separated from the sample and ionized, producing an ion beam. A series of MRM transitions read from the duty cycle list are executed on the ion beam by the tandem mass spectrometer. When at least one sentinel transition of the first group is detected, a next group identified by the sentinel transition is placed on the list.