Hi Jason,
The option to exclude ragged ends affects how the enzyme digestion works, but Skyline doesn't record whether a ragged end gets included in a peptide, or, more mysterious, whether cleavage happened at a "ragged" cleavage point. e.g.
...RLACKRMLLCIDER...
Could produce:
LACK
MLLCIDER
If you were not allowing missed cleavages, and you would have no way of knowing that both peptides result from a "ragged end" cleavage around the KR.
Yep. Interesting. If it is important I could add it to the TODO list, but, unfortunately, no indication of this case is even calculated let alone stored or presented in the report fields.
Let me know, if you would like to see this on the issues list. I can see how it would be useful.
--Brendan |
Maybe add it to the TODO list, but low priority. One of my reviewers wanted to know what all the ragged end peptides were. We can figure this out pretty easily, but I figured if skyline could do it, it’d be even easier! I think it would be nice to have that information occasionally.
Jason |