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No target proteins after FASTA import

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No target proteins after FASTA import lincolnh  2025-03-13 08:42
 

Hi Skyline team,
I am trying to set up a Skyline doc using a standard fasta, some mzML files and a custom blib file. During the "Import FASTA" step, I get the following error message:

Importing the FASTA did not create any target proteins

I've uploaded the blib to the file sharing portal, it's called ljh-cust-lib.blib. This blib was generated by applying BlibBuild to a handmade .ssl file. It's entirely possible that something is off with the blib, but I'm not sure what. I don't think the problem is with the fasta or mzML files -- I've used them to create Skyline docs many times.

Thanks for the help,
Lincoln
 
 
Nick Shulman responded:  2025-03-13 08:52
Title: No target proteins after FASTA import.
I think the most likely cause of that error would be that you have told Skyline to only include peptides from your spectral library and none of the spectral library peptides can be found in that FASTA file.
That is, the answer "Pick peptides matching" to on the "Library" tab "Settings > Peptide Settings" is "Library" (or maybe "Library and Filter").
If you want Skyline to include peptides that might not be in the library you could change that setting to "Filter" or "Library or Filter".

If you want to add all of the peptides from your spectral library to your document regardless of whether they can be found in a FASTA file you can go to the library explorer with the "View > Spectral Libraries" menu item (that menu item has moved to "View > Libraries > Library Explorer" in Skyline-daily) and ten press the "Add All" button.
After you have added peptides in that way you can organize them by protein using the "Refine > Associate Proteins" menu item.

If you are still having trouble you can send us your Skyline document and FASTA file.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries.

Files which are less than 50MB can be attached to these support requests.
If your .sky.zip and/or your FASTA file are larger than that you can always upload them here:
https://skyline.ms/files.url
-- Nick
 
lincolnh responded:  2025-03-13 12:24
Title: No target proteins after FASTA import

Hi Nick,
After some digging I suspect that this problem is coming from not having a scan field in the ssl file (which I then convert to blib and import into Skyline). Or more specifically, my .ssl has a scan field but every value is just NaN. Does that make sense?

In the meantime I'll give the workaround you suggested a try. Ultimately it would be great if we could do this through a standard Skyline import though.
Thanks,
Lincoln