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How can I analyze my data if there is no match in the library?

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How can I analyze my data if there is no match in the library? makhaik  2026-03-31 08:40
 

Hello
I am trying to analyze peptides for a few proteins using PRM which have no corresponding peptides available in library. Is there a way in which I can see what ions appear for the peptides? Thank you for your help.
 
 
Brian Pratt responded:  2026-03-31 09:45

You can start with a FASTA file (File > Import > FASTA), Skyline will create targets from the predicted the peptides and fragments.
 
makhaik responded:  2026-03-31 11:17

Thanks for your response. I can do that, but will I am unable to see the chromatogram for the ions that supposedly appeared in my experiment. I do see peak area bar graphs for a few ions but no chromatogram. Thanks!
 
Nick Shulman responded:  2026-03-31 11:43
Can you send us your Skyline document?
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 might have been extracted.

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
-- Nick