Patent ID: 8916386

Claim:
A method of detecting post translationally modified peptides using mass spectrometry comprising: (i) providing a mass spectrometer comprising an ion source, a first mass filter or mass analyser, a collision, fragmentation or reaction device arranged downstream of said first mass filter or mass analyser and a second mass filter or mass analyser arranged downstream of said collision, fragmentation or reaction device; (ii) performing a relatively low resolution negative parent ion scan wherein a mass to charge ratio transmission window of said first mass filter or mass analyser is scanned whilst a mass to charge ratio transmission window of said second mass filter or mass analyser is fixed and monitoring for first fragment ions of interest having a first mass to charge ratio above a threshold; wherein if first fragment ions of interest are detected by reaching the threshold then said method further comprises: (iii) performing a relatively high resolution negative MS scan wherein a mass to charge ratio transmission window of either said first mass filter or mass analyser or said second mass filter or mass analyser is scanned whilst the other mass filter or mass analyser is operated in a non-resolving mode of operation; immediately followed by a step (iv) comprising switching the mass spectrometer to a positive ion mode and, based upon information determined from the negative ion mode scans and expected phosphorylation, determining with the mass spectrometer at least a first positive ion Multiple Reaction Monitoring channel corresponding to positive ions having a first positive charge state, a second positive ion Multiple Reaction Monitoring channel corresponding to positive ions having a second positive charge state and a third positive ion Multiple Reaction Monitoring channel corresponding to positive ions having a third positive charge state; setting and monitoring at least said first, second and third positive ion Multiple Reaction Monitoring channels and determining which Multiple Reaction Monitoring channel results in a highest intensity of observed ions; and determining a mass to charge ratio or charge state of parent ions which correspond with the Multiple Reaction Monitoring channel which resulted in the highest intensity of observed ions; and a step (v) of performing a MS/MS scan wherein a mass to charge ratio transmission window of said first mass filter or mass analyser is set so as to correspond with the a mass to charge ratio transmission window at which said first mass filter or mass analyser was set for the Multiple Reaction Monitoring channel which resulted in the highest intensity of observed ions, and wherein a mass to charge ratio transmission window of said second mass filter or mass analyser is scanned to detect post translationally modified peptides.