MS2 Quantitation with Orbitrap ddMS2 Data

MS2 Quantitation with Orbitrap ddMS2 Data johnny perez28236  2022-11-21

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!


Nick Shulman responded:  2022-11-21
If you go to:
Settings > Transition Settings > Instrument
and check the checkbox that says "Triggered chromatogram acquisition" then Skyline will look at all of the chromatograms for a particular precursor and figure out whether any of those chromatograms have gaps in them, and, if so, excise those same gaps from all of the other chromatograms for that precursor.
You can also achieve the same effect by going to:
Settings > Transition Settings > Full Scan
and changing "MS/MS filtering Acquisition Method" to "SureQuant".

You can learn more about Skyline's triggered acquisition feature which was added to support Thermo SureQuant methods here:

After you change the transition settings, you will need to tell Skyline to extract chromatograms again by going to "Edit > Manage Results > Reimport".

-- Nick