Hi Brendan,
I was wondering if it is possible to use Skyline to analyze TopDown data. I found the limit is 200 amino acids for your peptide chain. Is it possible to increase this number? Also it would be interesting to have possibility to analyze not digested proteins. Usually we analyzing proteins up to 30kDa.
Thanks you for any help.
Best
Jacek

I think the number you are talking about is the maximum "peptide length" for applying a protease enzyme, but it sounds like you want to work with entire proteins without digestion at all. Do I have that right? Or are you wanting to measure very large peptides with some very limited protease cleavage that produces very large peptides? Is there any systematic cleavage rule being applied in your case?

I am able to add entire proteins as peptides using Edit > Insert > Peptides. I just did this for MAPK1. Worked great.

Since no response, I think we are just going to stick with Edit > Insert > Peptides as the solution here.