FAQ: What happens to my protein after deglycosylation?

When N-glycans are released with PNGaseF, the asparagine residue will lose an amino group and becomes aspartic acid. If other endoglycosidases were used (EndoH, Endo S, etc), a single GlcNAc residue (plus or minus a fucose if present in the N-glycan core) will remain attached to the asparagine. When O-glycosidase is used, serine and threonine residues that used to carry an O-glycan have no modification (in some applications, H218O is used to leave a trace on the amino acids where the O-glycan was removed).

The protein (native or denatured) remains in the reaction mixture along with the free sugars, where it is stable to be analyzed or isolated for downstream applications.