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Glycopeptides

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Glycopeptides ceren kul  2025-01-14 10:29
 

I would like to perform data analysis using Skyline for a while. I am trying to visualize specific glycopeptide precursors and the transitions corresponding to specific sugar masses. I can add glycopeptides along with their sugar compositions and visualize their transitions. However, after adding the glycopeptides, I cannot view only the Q3 sugar mass transition in MRM mode. For example, the precursor (Q1) mass of the glycopeptide is 1129.59 m/z, and the transition (Q3) mass is 366.14 m/z. I had entered these specific masses in the MRM method, but I am currently unable to view this data in Skyline. I hope there is a solution for this issue in Skyline, and I appreciate your response in advance.
 
 
Brian Pratt responded:  2025-01-14 10:40

Can you provide the transition list you imported to Skyline, and the resulting Skyline document (use File > Share to create a .sky.zip file), and the raw mass spec data? With those in hand we can probably sort this out quickly.

You can upload to http://skyline.ms/files.url

Thanks for using the Skyline support board,

Brian Pratt
 
Nick Shulman responded:  2025-01-14 10:45
If you send us your Skyline document and your mass spec data files we can try to figure out 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.

That Share Document dialog gives you the option of including the raw mass spec data files, or you could send them to use separately.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url

I would also recommend looking at the Small Molecule Targets tutorial if you have not already:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_small_molecule
-- Nick