Importation error from Surequant MS2 data

Importation error from Surequant MS2 data fgourgue  2023-04-03

We are doing a Surequant analysis run with Heavy peptides spiked into biological samples. Basically what is happening is the Mass Spec is collecting 15-20 MS2 of the Heavy peptide but when we try to import the results into Skyline only maybe 6-8 MS2 are actually being imported. We thought it might be because of the mass shift but when we calculated the mass error it was only around 5ppm which was well within the mass error we select in the Skyline software. And we know the MS2 of the Heavy peptides are good because they are triggering an MS2 for the light peptide in the Surequant runs on the mass spec.

Windows 10 pro 64-bit PC

Nick Shulman responded:  2023-04-03
Can you send me your Skyline document and .raw file?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

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:
-- Nick
Nick Shulman responded:  2023-04-03
Thank you for uploading your Skyline document and .raw file.

I see that you have chosen "DIA" as the acquisition method and "All Ions" as the isolation scheme. This is the wrong setting for your data.
"All Ions" should only be used when the mass spectrometer really is fragmenting everything without isolation any precursor m/z. This would be appropriate for Waters MSe data, as well as GCMS.

Skyline has some great features for working with Thermo SureQuant data, but, unfortunately you cannot use those features with this data because the "Scan Description" on your spectra are in the incorrect format and that causes Skyline to ignore all of your spectra if the "Triggered chromatogram extraction" checkbox is checked at "Settings > Transition Settings > Instrument".
Some of the "scan description" values in your raw file look like:
There is an explanation of what the scan description needs to look like at the bottom of the following support request:

Do you know why the scan descriptions in your raw file are set the way that they were? If you remove all of the scan descriptions from your method, then you will be able to use the "Triggered chromatogram extraction" checkbox in Skyline.
Where did you get your method from? If there was a mistake in any method file that you downloaded from Thermo we should let them know so that they can fix it.

If you are able to fix the "scan description" problem then I would recommend that you go to:
Settings > Transition Settings > Full Scan
and choose "SureQuant" for the MS/MS filtering acquisition method.
If you are not able to fix the "scan description" problem then I would recommend that set the acquisition method to "PRM" and make sure that "triggered chromatogram acquisition" checkbox at "Settings > Transition Settings > Instrument" is unchecked.

If you would like to learn more about SureQuant integration in Skyline I recommend the following page:

-- Nick