Interpretation of Glycan Spectra
Recent innovations in bioinformatics software have enabled a MS-based workflow (Figure 1) that accelerates glycan characterization through automated interpretation of the MSn data produced by ion trap and hybrid ion trap Orbitrap™ mass spectrometers (Thermo Fisher Scientific). This data is essential to resolving glycan heterogeneity and isomeric forms unequivocally.
As shown in Figure 1, MS/MS spectral fragmentation data is acquired on the ion trap or Orbitrap mass spectrometer and then imported into SimGlycan® software (Premier Biosoft). SimGlycan software automatically matches the experimentally acquired mass spectra against its database of theoretical glycan fragments, and generates a list of candidate glycan structures.
The SimGlycan database is a relational database containing 22,456 glycans, 22,814 glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan-related enzymes and 22,265 other database links. The database is continuously updated as new information on glycans is published.
Each proposed glycan structure is assigned a rank and a score to reflect how closely it matches the experimental data. The rank is based on calculating the proximity score, which is a numerical representation of how closely the experimental properties of the glycan, such as composition and branching pattern, match with those of the glycans in the database.