importing peptide search

importing peptide search ssedigh2  2023-07-25 09:20

Hi ,
when importing peptide search I keep having this error pop up , how do I fix it ?
"importing the FASTA did not create target proteins"
thank you,

Brian Pratt responded:  2023-07-25 10:22

If you can provide your Skyline document (use Skyline's File|Share menu item) and all the files you're using in the import, we can help you figure this out. You can upload to or someplace more private if you prefer.

Thanks for using the Skyline support board,

Brian Pratt

ssedigh2 responded:  2023-07-25 11:21

Hi Brian,
I have uploaded the files( name TMT)
thank you,

Nick Shulman responded:  2023-07-25 12:46

Thank you for uploading the file "TMT.rar".
I think the reason that you do not end up with any peptides in your document is that all of the peptide spectrum matches in your peptide search results have modifications that Skyline does not understand.
I see a lot of modifications with the mass 304.207146. Do you know what modification that is?

When you are doing the "Import Peptide Search" wizard, you can click "Cancel" when you get to the page where Skyline is asking for the FASTA file.
Then, you can go to:
View > Spectral Libraries
and see the spectral library that Skyline created from your peptide search results.

Skyline will tell you about all of the modifications which are in the spectral library which Skyline does not understand.

Skyline needs to understand all of a peptide's modifications in order to be able to add that modified peptide to your document.
-- Nick