Hi,

I have previously added peptide and protein information by “insert peptides”, and I only input peptide sequence and corresponding protein name. So there is no fasta information relating to the proteins. And I have finished all the peak manual check and boundary refining. Is there a way I can re-import the fasta information and correlate the information to the protein name?

I know I can insert Fasta and get all the protein information and relating peptide, however, in this case, Skyline will re-define the boundary, and then I need to re-analyze them, which is very tedious.
Thanks much for your help!
Have a good day!

Chaochao

This has definitely been a headache for people. It would really be nice to be able to add protein associations after peptides have been added using the "peptide list" mechanism. Currently, if you don't do this at the start, it is not really possible to do it later, without losing information, like annotations and manual integration.

This could be implemented as a simple form accessed from the Edit > Refine menu, say "Assign Proteins".

Then Skyline would look for matches between the peptide list names and the background proteome. If it finds matches, then it shows a form with a message.

This will assign sequences to [n] proteins in the document.
<This will leave [n] peptide lists without sequence information.> (only if the number is non-zero)

[OK] [Cancel]

If no matches are found, show a message like:

No proteins matching the names in the document were found in the background proteome.
Rename the proteins in the document or update the background proteome.

[OK]

There are also several other error cases the code would need to handle, like:

This feature requires a background proteome with names matching the protein names in your document.
Add a background proteome in the Peptide Settings - Digestion tab.

[OK]

The document contains no proteins without sequence information.

[OK]

This feature would be much appreciated, and hopefully not that difficult to implement.