Patent ID: 7112784

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 from said second sample are fragmented into one or more fragment ions and a low fragmentation mode wherein substantially fewer parent ions are fragmented; recognising first parent ions of interest from said first sample; automatically determining the intensity of said first parent ions of interest, said first parent ions of interest having 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 of interest with the intensity of said second parent ions.