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.
Best,
Kaifei Wang |