Fluorescently labelled N-glycans were separated by hydrophilic interaction liquid chromatography (HILIC) on Acquity UPLC H-Class instrument (Waters, USA) consisting of a quaternary solvent manager, sample manager, and a fluorescence detector, set with excitation and emission wavelengths of 250 and 428 nm, respectively. The instrument was under the control of Empower 3 software, build 3471 (Waters, Milford, USA). Labelled N-glycans were separated on a Waters BEH Glycan chromatography column, with 100 mM ammonium formate, pH 4.4, as solvent A and ACN as solvent B. In the case of IgG N-glycans, separation method used linear gradient of 75–62% acetonitrile at flow rate of 0.4 ml/min in a 27-min analytical run. For plasma protein N-glycans separation method used linear gradient of 70–53% acetonitrile at flow rate of 0.561 ml/min in a 25-min analytical run. The system was calibrated using an external standard of hydrolysed and 2-AB labelled glucose oligomers from which the retention times for the individual glycans were converted to glucose units (GU). Data processing was performed using an automatic processing method with a traditional integration algorithm after which each chromatogram was manually corrected to maintain the same intervals of integration for all the samples. The chromatograms were all separated in the same manner into 24 peaks (GP1–GP24) for IgG N-glycans and 39 peaks (GP1–GP39) for plasma protein N-glycans and are depicted in Supplementary Fig. 2 and Supplementary Fig. 3, respectively. Detailed description of glycan structures corresponding to each glycan peak is presented in Supplementary Table 1. Glycan peaks were analysed based on their elution positions and measured in glucose units, then compared to the reference values in the “GlycoStore” database (available at: https://glycostore.org/) for structure assignment. The amount of glycans in each peak was expressed as a percentage of the total integrated area. For IgG N-glycans, in addition to 24 directly measured glycan traits, eight derived traits were calculated (Supplementary Table 2). In the case of TwinsUK cohort, IgG N-glycan derived traits were calculated from plasma protein glycan profiles, based on known elution positions of predominat IgG N-glycan structures (Supplementary Table 3). In general, derived glycan traits average particular glycosylation features, such as galactosylation, fucosylation, bisecting GlcNAc and sialylation.

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