Extended Data Fig. 3: Profiling the glycoproteomic changes in SARS-CoV-2 infection by OxoScan-MS.
From: Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics
a. Gas-phase fractionation of a single commercial plasma tryptic digest over the precursor range m/z 500-2000 (in 3 separate runs, shown aggregated here) shows the optimum range for detection of glycopeptides by OxoScan-MS. b. Median CV (%) values for each feature quantified in clinical samples. CVs were calculated for each feature in triplicate measurements of each patient/donor sample, the median taken for each feature, ranked and plotted against feature number. Dotted line shows the CV = 20% threshold. c. Comparison of retention times for glycopeptides identified in both DDA (nano-flow, x axis) and DIA (micro-flow, y-axis) shows good agreement across different chromatographic platforms. d. Volcano plots comparing log2(fold-change) for all glycopeptide features between each grouped disease severity (mild, moderate, severe) against healthy controls. Log2(fold-change) and p-values were calculated using the limma R package3. Multiple testing correction was performed by the Benjamini-Hochberg method4. Coloured points represent those with |log2(fold-change)| > 1 and P < 0.05) for up- and down-regulated features (red and blue respectively).
