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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. 2 — a, Oxonium ion profiling workflow, starting with the generation of oxonium ion maps from unenriched tryptic digests of serum/plasma (glyco)proteins and computational analysis. b, An oxonium ion map of human plasma tryptic digest, extracted for the m/z = 204.09 (HexNAc) oxonium ion. Each spot represents a glycopeptide in a specific charge state. c, Oxonium ion maps for two common oxonium ions present in tryptic digests of human plasma, with and without treatment with a mix of glycosidase enzymes (bottom and top panels, respectively). Peak intensity is proportional to opacity, and all panels are scaled to the maximum peak intensity across the experiment. d, Comparison of intensities between two injections of human plasma tryptic digests. Spearman correlation coefficient was calculated on the basis of glycopeptide feature intensities (n = 1,006). e, log₂(fold-change) plotted for serum glycopeptide features from spiking in 3 different concentrations into an E. coli tryptic digest (n = 819). Fold-changes were calculated to a reference dilution factor of 1 and theoretical log₂(fold-change) values expected for each dilution factor are plotted as dashed lines. The box-and-whisker plots display 25th, 50th (median) and 75th percentiles in boxes; whiskers display upper/lower limits of data (excluding outliers, not plotted). Figure 2a created with BioRender.com.