Greetings, I am a pfind user from Zhiyong's group in Carnegie Institution for
Science. I am trying to use pfind to analyze o-glycosylation modifications of
my proteins. O-glycosylation, such as O-GlcNAc which is included in my search
parameter (HexNAc S/T), is usually labile and in my HCD data is expected to
result in neutral loss and the exact positions of modifications are mostly not
identifiable. I am surprised to find that all O-glycosylation have been
assigned a modification site and there is no neutral loss. In the example in
the attached pdf, HexNac is assigned to the first serine. The y/b ions do not
seem to provide enough information to make this assignment, could you please
explain to me how the site assignment is calculated? Also, over 1000 peptides
are identified to be O-glycosylated, but none shows neutral loss, does pfind
filter those out? Thank you in advance for your help. |