Patent ID: 6982414

Claim:
A method of mass spectrometry comprising: passing parent ions from a first sample to a fragmentation device; repeatedly switching said fragmentation device between a high fragmentation mode wherein at least some of said parent ions from said first sample are fragmented into one or more fragment ions and a low fragmentation mode wherein substantially fewer parent ions are fragmented; passing parent ions from a second sample to a fragmentation device; repeatedly switching said fragmentation device between a high fragmentation mode wherein at least some of said parent ions are fragmented into one or more fragment ions and a low fragmentation mode wherein substantially fewer parent ions are fragmented; automatically determining the intensity of first parent ions from said first sample which have a first mass to charge ratio; automatically determining the intensity of second parent ions from said second sample which have said same first mass to charge ratio; and comparing the intensity of said first parent ions with the intensity of said second parent ions; wherein if the intensity of said first parent ions differs from the intensity of said second parent ions by more than a predetermined amount then either said first parent ions and/or said second parent ions are considered to be parent ions of interest.