Input data

Input data asamaras  2022-04-11


My name is Tasos and I a new user of Skyline. I have a problem with a protein list input. My goal is to insert a protein list with 854 proteins in a fasta file. The goal is to find the predicted peptides of these proteins after trypsin digest. The problem that I have is that when I insert my protein list, I can see predicted peptides only to the first 5 proteins in the list, but if you click to the other proteins you can see them. But if you just see the list you can't see them. This could be a limitation of the software in the number of the proteins?
Thank you in advance for your help.

Best regards,
Samaras Tasos

Nick Shulman responded:  2022-04-12
The usual way to add a FASTA file to Skyline is with the menu item:
File > Import > FASTA...

Skyline will digest the proteins in the FASTA file based on the enzyme you have selected at:
Settings > Peptide Settings > Digestion

The set of peptides that you end up getting is also affected by the settings that you might have on the "Filter" or "Library" tabs of the Peptide Settings dialog, and also can be affected by the settings at "Settings > Transition Settings > Filter"

I am not sure I understand what might be going wrong for you. If you would like, you can send us your FASTA file and your Skyline document and we might be able 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.

If that .zip file and/or your FASTA file are less than 50MB you can attach them to this support request. You can upload larger files here:
-- Nick