Hi Carmen,
I suspect you have chosen to exclude "ragged ends" in the Peptide Settings - Filter tab. If you look closely at the range you have highlighted, it is filled with consecutive cleavage sites (KK, RR, KR, RK). And in fact, the peptide you are highlighting with a red box can only be formed by cleaving between K and R at the N-terminus.
If you uncheck this checkbox in your settings, I expect you will get closer to what you are expecting. Then you just have to decide if that is really what you want.
Thanks for the helpful screenshots.
--Brendan |
Dear Brendan,
You are right, that was the issue. After unchecking this box, I can see all the peptides.
Many thanks for your help, really appreciated.
Carmen |