FragPipe-PDV viewer of intact glycopeptide

[ming-bi]

- Describe the issue or question:
I applied fragpipe to searching N-glycopeptide and the results were opened in PDV viewer. But I am confused about the sepectrum. Taking the followed pciture as an example, the last fragment ion was modified six HexNAc. What is the meaning of this fragment ion?

[KaiLiCn]

Hi,

Please use the NIH Glycan symbol as the reference https://www.ncbi.nlm.nih.gov/glycans/snfg.html. The structure is just for the visualization, not the real structure.

Kai

[ming-bi]

thank you for your answer.
The last fragment ion is it ture? This ion represents a Y ion of glycopeptide. Is it correctly matched the compositon?

[KaiLiCn]

Yes. The last peak was matched to a charge +2 Y ions with the composition shown in the spectrum. You could see the peak m/z putting the cursor on the peak. Please let us know if the mass is incorrect. The mass error should be within your searching tolerance.