Show Modified Sequence Missing romeally  2019-09-11 08:00
 

I am trying to do quant on modified peptides and the one webinar says to treat them as proteins to do replicates and get statistics to work. I have done this and it works but for some reason I can't get my final report to show the modified sequence in the table (see attached). I would like the final report to show this since any name for the protein is less than descriptive. Am I not defining something correctly in my document grid?
Thanks!
Bob
 
 
Nick Shulman responded:  2019-09-11 10:57
The group comparison feature in Skyline allows you to choose whether to calculate the fold changes at the Protein level or a the Peptide level.

On the "Edit Group Comparison" dialog, there is a group of buttons labeled "Scope" where you can choose "Protein" or "Peptide".

If you are calculating fold changes at the Protein level then the peptide-related columns will always be blank.
-- Nick
 
romeally responded:  2019-09-12 12:28
Yes that's it! I was following the webinar #9 where he named the peptides as proteins and that messed me up. I overlooked the Scope tab and thought that was how it was done. Fixed thanks!