target GlyScore pep is none

[congcongW]

I wonder if the pGlyco2 can identifi glycopeptide deglycosylated by PNGase F in 18O-water. there are Deamidated_18O(1)[Q] but no Deamidated_18O(1)[N] in the step of Identification.Thank you!

when I select the Deamidated_18O(1)[Q], output show : pGlyco Info] License will be expired in 2019/01/01 [pGlyco Info] Loading glycan database ... [pGlyco Info] Ion Indexing ... [pGlyco Info] G:\WCC\pGlyco\20180811_NGlyco_8_HCDFT.mgf Process 1: [I.D.] 100.0% [==================================================] [pGlyco Info] G:\WCC\pGlyco\20180811_NGlyco_8_HCDFT.mgf finished! Process 1: [Complete] 100% [==================================================] [pGlyco Info] Estimating FDR ... Fitting glycan part ... target GlyScore pep is none Fitting peptide part ... [pGlyco Info] Inferring proteins ... Reading pGlyco results ... [pGlyco Info] Combining all results to: ----C:\Users\Acer\Documents\pGlyco\pGlyco_task_2018-11-27-11-45-55\pGlycoDB-GP-FDR-Pro.txt [pGlyco Info] Task Complete!

and the summary

Total MS2 Scans = 66528

---- # Contained Scans = 98 ---- Ratio = 0.00147306

[jalew188]

@congcongW It seems that there are few oxonium contained MS/MS spectra for glycopeptide identification.

[congcongW]

I know pGlyco is for intact glycopeptides,including both the glycan and the peptide. But could pGlyco used for only glycosite-containing peptides not intact N-glycopeptides ? MS/MS acquisition only include the peptide. Because N-linked glycans been released from glycopeptide by PNGase F digestion in experimental procedures.Thank you！

[jalew188]

@congcongW Not necessary, peptide search engines can search de-glycosylated peptides. You can use pFind or MaxQuant.