Patent ID: 8618474

Claim:
A method of analyzing analytes in a sample when the number of analytes of interest to be scanned in an experiment exceeds the number of analytes that can be scanned within a duty cycle and still maintain acceptable data quality, the method comprising: (a) emitting ions from the sample; (b) selectively filtering ions emitted from the ion source for ions stored in a duty cycle list during each cycle by controlling the first mass filter to filter for a precursor ion on the duty cycle list and controlling the second mass filter to filter for a corresponding fragment ion on the duty cycle list; and (c) limiting the number of ions on the duty cycle list for each cycle by adding trigger precursor ions and corresponding trigger fragment ions from one or more stored trigger data sets that have trigger time windows that include the current cycle time to the duty cycle list, removing trigger precursor ions and corresponding trigger fragment ions that have trigger time windows that do not include the current cycle time from the duty cycle list, when a trigger fragment ion is detected by the detector, adding any confirmatory precursor ions and corresponding confirmatory fragment ions from one or more stored confirmatory data sets designated by the trigger data set of the detected trigger fragment ion to the duty cycle list, and removing confirmatory precursor ions and corresponding confirmatory fragment ions that have trigger time windows designated by trigger data sets of detected trigger fragment ions that do not include the current cycle time from the duty cycle list, wherein a trigger data set has at least one trigger entry, wherein each trigger entry includes a designated trigger ion, a designated trigger ion fragment, a trigger time window, and a confirmatory data set, wherein each confirmatory data set has at least one confirmatory entry, and wherein each confirmatory entry includes a designated confirmatory ion, and a designated confirmatory ion fragment.