MS2 Quantitation with Orbitrap ddMS2 Data | johnny perez28236 | 2022-11-21 07:52 | |||||||||
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. Thanks again! Johnny |
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