|MS2 Quantitation with Orbitrap ddMS2 Data
Good Morning, I hope this email finds you well.
I am using Skyline to interpret ThermoFisher Exploris data. My method performs SIM analysis followed with MS2 analysis if about a certain ion threshold. What I have noticed is that Skyline extrapolates data for the entire LC run time. Therefore, if the ddMS2 data was only collected for 30 seconds and the run is 5 minutes, it will extrapolate the baseline from 0 - 5 minutes. See attached picture. This causes a problem when attempting integration. Is there any way to prevent skyline from doing this?
I've also attached what ThermoFisher's qualitative analysis software shows for the same MS2 experiments.