Network Method for Building a Sample-Specific Glycan Database for N-Linked Glycosylation from MS/MS Data

Mass spectrometry is widely used for studying proteins and glycoproteins. For glycoproteins, successful data interpretation using database search requires a complete glycan database─a condition that is often not satisfied. We present here software that builds improved glycan databases by constructing a sample-specific glycan database based on the mass spectrometry data itself, rather than relying solely on existing glycan databases. Rather than analyzing individual spectra in isolation, our GlycoNetworks software constructs a network of putative glycans where each node represents a glycan and each edge represents a monosaccharide or other building block. To test the performance of GlycoNetworks, we reanalyzed several data sets from public mass spectrometry repositories and showed that GlycoNetworks is able to discover new glycans that the original publications missed.