FAQ: Can I fluorescently label a glycan released with endoglycosidases?

Yes, since a reducing end is intact on the released glycan, making the carbohydrate ready for labeling by reductive amination with the fluorescent group of choice. Notice that PNGaseF is an amidase: in that case an amino group is left attached to the end of the glycan, but it is extremely labile at pH< 8.5. The amino group is immediately lost after the glycan is released (under typical conditions at pH 7.5) leaving a free reducing end ready for reductive amination.