1. If the modifications are known, I think it would be more appropriate to use 
pGlyco 3.
2. pGlyco 3 has visualisation capabilities.
3. Is the third question to discover unknown modifications? Maybe pChem software 
will meet your needs.

The relevant software can be found at http://pfind.org/software.html.

Dear teacher,
I have the following questions about p-Find and p-Glyco:
1. We want to customize a modification to search for N-glycopeptides enriched by 
chemical reaction by clicking on them. Which software is more appropriate to use 
p-Find or p-Glyco?
2. How do I use p-Glyco or p-Find to view glycosylation sites?
3. Which software can customize the new retouching? How to customize? Is it to 
calculate the Mass number of the modification?