I digest a glycoprotein (with known glycosylated site N34)and its unglycosylated form with Trypsin Gold. When I took MALDI for both, the glycosylated form show almost exactly same peaks as found in the unglycosylated one except the fragment containing N34 and this is normal because N34 is glycosylated. However, I can't find the corresponding fragment with sugar side-chain either. I repeated and got the same result.
Do you have any idea what went wrong? What other method can I use to find the glycosylated site?
How can I confirm the glycosylated site using MALDI?
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