Integrating HexNAcQuest with Glycoproteomics Data Analysis Software to Distinguish HexNAc Isomers on Peptides.

Recently, HexNAcQuest was developed to help distinguish peptides modified by HexNAc isomers, more specifically O-linked β-N-acetylglucosamine (O-GlcNAc) and O-linked α-N-acetylgalactosamine (O-GalNAc, Tn antigen). To facilitate its usage (particularly for datasets from glycoproteomics studies), herein we present a detailed protocol. It describes example cases and procedures for which users might need to use HexNAcQuest to distinguish these two modifications.