OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale

Abstract

Protein glycosylation is a complex and heterogeneous post-translational modification. Specifically, the human plasma proteome is rich in glycoproteins, and as protein glycosylation is frequently dysregulated in disease, glycoproteomics is considered an underexplored resource for biomarker discovery. Here, we present OxoScan-MS, a data-independent mass spectrometric acquisition technology and data analysis software that facilitates sensitive, fast, and cost-effective glycoproteome profiling of plasma and serum samples in large cohort studies. OxoScan-MS quantifies glycosylated peptide features by exploiting a scanning quadrupole to assign precursors to oxonium ions, glycopeptide-specific fragments. OxoScan-MS reaches a high level of sensitivity and selectivity in untargeted glycopeptide profiling, such that it can be efficiently used with fast microflow chromatography without a need for experimental enrichment of glycopeptides from neat plasma. We apply OxoScan-MS to profile the plasma glycoproteomic in an inpatient cohort hospitalised due to severe COVID-19, and obtain precise quantities for 1,002 glycopeptide features. We reveal that severe COVID-19 induces differential glycosylation in disease-relevant plasma glycoproteins, including IgA, fibrinogen and alpha-1-antitrypsin. Thus, with OxoScan-MS we present a strategy for quantitatively mapping glycoproteomes that scales to hundreds and thousands of samples, and report glycoproteomic changes in severe COVID-19.

Connecting single-nucleotide polymorphisms, glycosylation status, and interactions of plasma serine protease inhibitors

“…Of recent interest, genomic and glycoproteomic studies of recovered COVID-19 patients revealed that fucosyltransferases and plasma glycoprotein fucosylation levels are associated with critical illness from COVID-19. 37 , 38 , 39 Based on our results, we speculate that additional fucose residues on SERPINA1 may regulate SERPINA1-TMPRSS2 interactions. As a consequence, these additional residues may therefore affect TMPRSS2-mediated SARS-CoV-2 spike protein priming and viral infection.…”

Hydrophilic interaction chromatography coupled to ultraviolet photodissociation affords identification, localization, and relative quantitation of glycans on intact glycoproteins

“…28 Electron-based and collision-based MS/MS methods may be paired to provide peptide sequence, glycan identification, and glycosite localization of glycopeptides, [54][55][56] and have been used in an integrated manner for countless high throughput bottom-up glycoproteomics studies. 17,20,49,57 For top-down analysis of glycoproteins, the use of high-performance mass spectrometers is essential for the accurate identification of fragment ions, as demonstrated in a recent study that combined CAD and ECD to achieve characterization of glycan structures, glycosite locations, and some of the O-glycoform microheterogeneity of the SARS-CoV-2 spike protein RBD, albeit without chromatographic separation of glycoforms. 28 An alternative high-energy activation method, ultraviolet photodissociation (UVPD), has shown success in identifying and localizing glycans on peptides.…”