Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics

<p>Protein glycosylation &mdash; a complex and heterogeneous post-translational modification frequently dysregulated in disease &mdash; has been difficult to analyse at scale. Here we report a data-independent-acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named &lsquo;OxoScan-MS&rsquo;, identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive, untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from COVID-19 patients and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.</p>