Molecular Modeling of Cation Coordination to Glycopeptides and Its Implications in Mass

Mass spectroscopy is an often-used technique to identify compounds, as the name indicates, by their mass. However, molecules must be charged to be detected in mass spectrometry, thus ionization is necessary. Sometimes ionization is accomplished by coordination of an ion with a molecule. When attempting to understand chemistry at this level it is difficult, if not impossible, to investigate the subject of interest directly, so molecular modeling is used. Research on glycoproteins is active, specifically studying the effects of the glycans on immune system activation and protein folding. The research investigated how different ions coordinated to various glycopeptides during mass spectroscopy by comparing theoretical modeling and experimental data. It was observed experimentally that sodium tended to coordinate with the glycan portion, while protons favored the peptide. The molecular modeling results have shown that this is due to sodium's large size, resulting in affinity towards the many oxygens of the glycan, and the proton's small size, allowing it access to the most basic site. Understanding these trends allows for better interpretation of mass spectra. Molecular modeling provides a more complete understanding of how ions coordinate during mass spectrometry, and consequently why some mass spectral patterns are observed.