Author beyond
Recipients beyond
Date 2021-10-14.14:13:09
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.
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