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Regarding glycoproteomic analysis via proteome discoverer by Orbitrap Fusion Tribrid MS

Involved Contributor
Involved Contributor

I am a PhD scholar working in the field of proteomics. We are working in the field of determination of glycosylation changes responsible after diabetes induction. We are doing glycoproteomic analysis after enrichment in the biological fluid via Orbitrap Fusion Tribrid Mass Spectrometer and are employing Proteome discoverer 2.2 for data analysis. We are just getting the quantitative result after the analysis but our focus is to see the amount of glycosylation and type of glycosylation, which we are not able to get. We know that to get that byonic is the software but unfortunately, our institute can't purchase it for now. 

Can you just guide us that how we can achieve our aim of the study??

Any help at your end will be highly appreciated.

Thank You


Bhavneet Kaur


Team TFS
Team TFS

There are few free software that might meet your immediate needs. pGlyco has been recommended by number of experts in the field. It handles HCD and ETD fragmentations. It handles both N-linked and O-linked glycopeptides. Protein Prospector and MSFraggerGlyco are also free alternatives. This recent preprint did a comparison of number of software including few that were mentioned here. It might give you an idea of their performance.


In terms of quantitation I am not sure if there are free software that can do this. For a single protein BioPharma Finder can and I believe it can do for 50 or 100 proteins. It can identify and quantify N or O linked glycan attached to the peptides from Human and CHO databases.  The software does provide a way to determine the % abundance for each glycan. There is a 60 day free trial for it. You might download it to explore it. Hope this helps.

Team TFS
Team TFS

@Bhav1200 , I'm not sure if you know much about IC-MS but we have several application notes on characterization of O- and N-linked glycans for glycoproteins:

O-Glycan Profiling using HPAE-PAD Hyphenated with a High-Resolution Accurate Mass (HRAM) Mass Spectr...


HPAE-PAD profiling of N-linked oligosaccharides from glycoproteins using dual eluent generation cart...  

There are more info in