Multiplex Orbitrap Data - Cannot get Skyline to Recognize SIL Peptide Transitions

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Multiplex Orbitrap Data - Cannot get Skyline to Recognize SIL Peptide Transitions lamarj  2022-02-18
 

To whom it may concern,

We are trying to process data acquired with an Orbitrap Fusion Lumos. It looks like skyline has the correct predictions for transitions (we observe several in the .raw file, please see attached screenshot) but they are not being recognized/plotted in the chromatogram. I have tried just about everything I can think of in the transition settings. Skyline does "identify" non-labeled transitions, but transitions associated with the SIL peptides are not identified. Currently using version 21.2.0.369

Thanks,

Jason

 
 
Nick Shulman responded:  2022-02-18
The usual reason that you do not get chromatograms for your MS2 transitions is that no MS2 spectra matched the precursor. This usually depends on the settings that you have at:
Settings > Transition Settings > Instrument
and
Settings > Transition Settings > Full Scan

If you send us your Skyline document and one of your raw files, we will be able to tell you what is going wrong.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including whatever chromatograms may have been extracted.
If that .zip file and your .raw file are less than 50MB you can attach them to this support request. You can upload larger files here:
https://skyline.ms/files.url

-- Nick