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DIA analysis on SKyline: some peptide does not appear in raw extracted chromatograms.

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DIA analysis on SKyline: some peptide does not appear in raw extracted chromatograms. bioc1213  2023-09-07 02:41
 

Hi, After successful creating and importing the library and analyzing the raw file (DIA data) on Skyline, I can see most of the extracted chromatograms of the peptides which are present in library. I noticed that for some peptides the raw chromatograms do not appear even they are present in the library. Please see the screenshot. Can you please guide me how to resolve this issue.
 
 
Nick Shulman responded:  2023-09-07 05:57
The usual reason that chromatograms like this do not show up is that there were no MS2 spectra in the raw file which matched the m/z of your precursor.

Sometimes this has to do with the isolation scheme that you have specified at Settings > Transition Settings > Full Scan.

If you send us your Skyline document and one of your raw files we can tell you what is going on.

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/or 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