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Help With Tutorial haig baghdassarian  2023-10-08 21:48
 

Hello,
I am trying to go through the tutorial for targeted method editing and I cannot get past page 7. Every time I try copying and pasting the fasta contents into Skyline I keep getting an error stating, "This operation has added 35 new proteins with no peptides meeting your current filter criteria. Do you want to remove all empty proteins before showing the document?" I say to keep them, but then the protein names are listed but they are empty; no peptides. I have tried manually selecting the peptides for the proteins, but only the ones that I can see through the tutorial since I have no idea what the others are. Then, when I try copying the same material under "Insert > Proteins" or "Insert > FASTA" and paste the material into the table, it looks very chaotic and nothing is where it should be. I have even tried manually inputting a couple of entries and that still did not work for that part. I have watched online videos and have read the tutorial for this, but I have not gotten it to work. Is there someone I can talk to who can walk me through the process, maybe I am missing a step or inputting something incorrectly. Also, I have the most recent version of Skyline.
 
 
Nick Shulman responded:  2023-10-08 22:14
I tried these steps and it did work for me.
You are supposed to get a message box telling you that some of the proteins that have been added are empty. We should fix the text in the tutorial so that it tells you to expect that message box, and that you're supposed to push the "Keep" button.

The message box is supposed to say that 30 proteins will be empty (which means that 5 proteins will be non-empty). The "35" that you are seeing is unexpected.

At the beginning of the tutorial (top of page 2), it says that you should use the menu item:
Settings > Default
to reset the settings in the current document to the default values.
If you skipped that step, then I could imagine that the settings in your document might be incorrect, and you would not end up with the peptides you were supposed to.

If you send us your Skyline document, we can probably figure out what is going wrong. After you have pasted the FASTA file and things look wrong, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including the spectral library and background proteome.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick