Missing peptides pop-up pick list

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Missing peptides pop-up pick list carmen.gonzaleztejedo  2018-05-09 02:49
 

Dear Brendan,

I have a doubt regarding the list of peptides that are shown in the pop-up pick list for a specific protein. Are they unique peptides? Sometimes, it's not showing the whole list of peptides for the protein (see attached). In my case, for protein Q96BR1. peptides contained between 42 and 102 positions are not available to pick. As you can see, I have used a Human background proteome, but I haven't enforced any type of uniqueness. Why is that happening then?

Many thanks in advance,

Carmen

 
 
Brendan MacLean responded:  2018-05-09 05:35
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
 
carmen.gonzaleztejedo responded:  2018-05-09 07:18
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