N -linked Glycan Release Efficiency: A Quantitative Comparison between NaOCl and PNGase F Release Protocols.

There are several methods, both chemical and enzymatic, to release -linked glycans for structural characterization. One of the most common enzymatic release methods is the use of peptide:-glycosidase F (PNGase F). A less expensive and quicker alternative has been reported for the release of -linked glycans chemically using sodium hypochlorite (NaOCl), which hydrolyzes the peptide-glycan bond, yielding the intact glycan with a free reducing terminus. Here, we quantitatively analyzed the efficiency of the NaOCl release protocol compared with the PNGaseF release protocol for small-scale analysis (300 µg) using liquid chromatography-single reaction monitoring-mass spectrometry. We determined that the relative glycan composition of released -linked glycans from the NaOCl protocol is similar to a typical PNGase F protocol, but the absolute recovery of -linked glycans is significantly lower with the chemical procedure.