initiator methionine peptide

initiator methionine peptide dkueltz  2016-01-11
I am trying to use N-terminal peptides for quantitation. The initiator met is cleaved off cotranslationally for many proteins and, as a result, the peptide is not properly recognized as a tryptic peptide by Skyline (since it is not preceded by a K or R but by M) if we digest the proteome with trypsin [KR | P]. When digesting the proteome with trypsin-CNBr [KRM | P] then cleavage also occurs at internal M and the corresponding peptides are incorrectly marked as having a missed cleavage. Is there any way to define a digestion scheme that is based on trypsin [KR | P] but also includes cleavage of the initiator methionine, which is common for many proteins? My lab is working on quantifying the N-terminal peptide because we study effects of enivronmental stress on N-terminal modification (acetylation, etc) of proteins.
Happy 2016!
Brendan MacLean responded:  2016-02-06
Hi Dietmar,
You are not the first to have requested this. I have posted this as an issue to our issues list:

With any luck we will implement a solution by the next public release. Sorry we don't already have this for you.

Thanks for your feedback!