Rationale
N‐glycosylation is one of the most common protein post‐translational modifications; it is extremely complex with multiple glycoforms from different monosaccharide compositions, sequences, glycosidic linkages, and anomeric positions. Each glycoform functions with a particular site‐ and structure‐specific N‐glycan that can be fully characterized using state‐of‐the‐art tandem mass spectrometry (MS/MS) and the intact N‐glycopeptide database search engine GPSeeker that we recently developed. Urine has recently gained increasing attention as a non‐invasive source for disease marker discovery. In this study, we report our structure‐specific N‐glycoproteomics study of human urine.
Methods
We performed trypsin digestion, Zwitterionic Hydrophilic Interaction chromatography (ZIC‐HILIC) enrichment, C18‐RPLC/nano‐ESI‐MS/MS using HCD with stepped normalized collisional energies, and GPSeeker database search for a comprehensive site‐ and structure‐specific N‐glycoproteomics characterization of the human urinary N‐glycoproteome at the intact N‐glycopeptide level. For this, we used b/y product ion pairs from the GlcNAc‐containing site‐determining peptide backbone and structure‐diagnostic product ions from the N‐glycan moieties, respectively.
Results
We identified 2986 intact N‐glycopeptides with comprehensive site and structure information for the peptide backbones (amino acid sequences and N‐glycosites) and the N‐glycan moieties (monosaccharide compositions, sequences/linkages). The 2986 intact N‐glycopeptide IDs corresponded to 754 putative N‐glycan linkage structures on 419 N‐glycosites of 450 peptide backbones from 327 intact N‐glycoproteins. Next, 146 linkage structures and 200 N‐glycosites were confirmed with structure‐diagnostic and GlcNAc‐containing site‐determining product ions, respectively.
Conclusions
We found 106 new N‐glycosites not annotated in the current UniProt database. The elution–abundance patterns of urinary intact N‐glycopeptide oxonium ions (m/z 138 and 204) of the same subject were temporally stable during the day and over 6 months. These patterns are rather different among different subjects. The results implied an interesting possibility that glycopeptide oxonium ion patterns could serve as distinguishing markers between individuals and/or between physiological and pathological states.