Patent ID: 7622712

Claim:
A method of operating a mass spectrometer system having an ion trap, the method comprising: a) processing a first group of precursor ions to obtain a first plurality of fragment ions trapped in the ion trap; b) applying a first encoding operation for encoding a first selected characteristic in at least one of the first group of precursor ions and the first plurality of fragments, wherein the first encoding operation is applied to the at least one of the first group of precursor ions and the first plurality of fragments without being applied to other ions such that the first plurality of fragment ions has the first selected characteristic and the other ions lack the first selected characteristic; c) ejecting the first plurality of fragment ions and the other ions out of the ion trap; d) detecting the first plurality of fragment ions and the other ions; e) based on the first selected characteristic, correlating the first plurality of fragment ions detected with the first group of precursor ions to distinguish the first plurality of fragment ions from the other ions detected.