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. 2023 Jul 20;8(3):233–247. doi: 10.1038/s41551-023-01067-5

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a, Plasma samples are measured using OxoScan-MS to generate oxonium ion maps, and glycopeptide features are identified with complementary fragmentation and database searching. OxoScan-MS then allows quantification of identified features across cohorts with >100s of samples. b, MS1 spectrum of tryptic plasma digest with Q1 profiles of oxonium ions overlaid. Oxonium ion traces localize glycopeptide precursor ions even in the presence of co-eluting unmodified peptides of significantly higher abundance. Inset shows zoomed-in oxonium ion traces with precursor m/z labelled on the x axis. Q1 profiles were acquired with a 2 m/z scanning window. Top: haptoglobin N-glycopeptide (Asn184). Middle: fibrinogen beta chain N-glycopeptide (Asn394). Bottom: immunoglobulin A N-glycopeptide (Asn340). c, Comparison of DDA (HCD) and DIA (CID) MS/MS spectra for respective glycopeptide precursors. Fragment assignments are taken from analysis of DDA data in Byonic (with a tolerance of 5 ppm for DDA and 20 ppm for DIA). Fragments observed in both DDA and DIA spectra (also matched to within 20 ppm) are shown in blue and oxonium ions are shown in red. All non-matched assignments are shown in grey. Respective panels show the same glycopeptides as in b. d, Oxonium ion elution profiles in both precursor m/z and RT space for respective glycopeptide precursors. Blue and red ellipses represent the quantification and exclusion regions, respectively, and the horizontal line indicates accurate (TOF) precursor m/z. Panels show the same glycopeptides as in b and c. Figure 4a created with BioRender.com.