N-Glycat Library

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N-Glycat Library maryam imaninejad  2022-08-15
 

Hello Skyline Team,

We started using InstantPC to label released mAb N-glycans to study and analyze N-glycans. For this purpose, a Waters QTof system and an MSe method were used. We could analyze our data using Skyline small molecule interface. However, this analysis was based on the precursor ion and its multicharges. As you know, some of the glycans have the same masses and using precursor ions will not let to differentiate these glycans. We are interested in using MSe and MS/MS data to correctly identify N-glycans. It seems that N-glycat library is the one that can help for this purpose. I could not find this library in your website. Not sure if it actually exists. If not, can you help us know how to use MSe data for correct ID? Is there any other library that can use MS1 and MS2 data to assign detected N-glycans? Most of the N-glycans that we are trying to identify is neutral or monosialylated.

Thank you,
Mary

 
 
Chris Ashwood responded:  2022-08-15

Dear Mary,

I was originally working on N-GlyCat (https://zenodo.org/record/3888990) but have since left that lab. Based on the public presentation at the link I provided, N-GlyCat did not support various glycan tags as the structural analysis platform was for reduced N-glycans only. Supported glycan types could have changed since I left, so contacting the PI (Rebekah Gundry) might be beneficial.

I do not know of any publicly available glycomics libraries for InstantPC-labeled N-glycans, so you may need to create your own.

Generally, if you have chemical formulae for the glycans you are interested in, you will be able to extract out the chromatogram for each glycan mass in Skyline. From there, you either need a series of product ions specific for a given glycan structure (diagnostic ions) or a reproducible retention time. As retention times are easier to implement for automated peak picking, that's my preferred option.

Happy to answer any of your questions, my glycomics work using Skyline is ongoing.

Cheers,
Chris Ashwood