Identification of Glycopeptides with Multiple Hydroxylysine O‑Glycosylation Sites by Tandem Mass Spectrometry

Glycosylation
is one of the most common post-translational modifications
in proteins, existing in ∼50% of mammalian proteins. Several
research groups have demonstrated that mass spectrometry is an efficient
technique for glycopeptide identification; however, this problem is
still challenging because of the enormous diversity of glycan structures
and the microheterogeneity of glycans. In addition, a glycopeptide
may contain multiple glycosylation sites, making the problem complex.
Current software tools often fail to identify glycopeptides with multiple
glycosylation sites, and hence we present GlycoMID, a graph-based
spectral alignment algorithm that can identify glycopeptides with
multiple hydroxylysine O-glycosylation sites by tandem mass spectra.
GlycoMID was tested on mass spectrometry data sets of the bovine collagen
α-(II) chain protein, and experimental results showed that it
identified more glycopeptide-spectrum matches than other existing
tools, including many glycopeptides with two glycosylation sites.