Author kfwang
Recipients beyond, kfwang
Date 2021-10-22.11:02:09
This question may require complicated explanations:
1. I'm not sure if you set the neutral loss when setting up the modification, 
guess you have completed the setting. Because the mass of neutral loss is equal 
to the modification itself, this is also in line with your description of the 
modification label.
2. pFind 3 currently does not have the function of modification site 
positioning, so it will try to score all S and T, and find the highest. In this 
case, when the modification is added to the far left, the effect on the y ion is 
minimal (the y ion is generally relatively stable and contributes a lot to the 
scoring), which will make the score the highest.
3. As for the 1000 peptides without neutral loss, I'm not sure about this, 
because I don't know what the quality of the spectra are. In pFind, these 
spectra will not be automatically filtered based on the neutral loss.

Kaifei Wang
Date User Action Args
2021-10-22 11:02:12kfwangsetmessageid: <>
2021-10-22 11:02:12kfwangsetrecipients: + kfwang, beyond
2021-10-22 11:02:12kfwanglinkissue48 messages
2021-10-22 11:02:12kfwangcreate