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. 2023 Apr 4;22(5):100540. doi: 10.1016/j.mcpro.2023.100540

Fig. 3.

Fig. 3

Differences in the N-glycoproteome of RA and OA synovium.A, cumulative number of N-glycopeptides identified in OA (n = 4) and RA (n = 4) samples. B, OPLS-DA score plots of N-glycoproteomics data of OA and RA synovium. C, volcano plot showing 67 upregulated and nine downregulated N-glycopeptides in RA (median ratio (RA/OA) >1.5 or <0.67 and Student’s t test, p < 0.05). D, scatter plot depicting the differences in N-glycopeptides and their corresponding proteins between OA and RA. The blue and green dots represent the median ratio (RA/OA) of each N-glycopeptide greater than 1.5 and less than 0.67, respectively. The dashed lines represent the median fold change of proteins at 1.2 and the median fold change of N-glycopeptides at 1.5. E, scatter plot shows the correlation of N-glycopeptides with fold changes greater than 1.5 in (C) before and after normalization to glycoproteins. The blue and green dots represent the normalized ratio (RA/OA) of each N-glycopeptide greater than 1.2 and less than 0.83, respectively. The gray solid line represents the line with slope 1. F, box plot shows the differences in N-glycopeptides in (C) without proteins identified in proteomics (Student’s t test, ∗p < 0.05; ∗∗p < 0.01). G, comparison of the distribution of N-glycans on the significantly changed N-glycopeptides. H, comparison of N-glycoproteins related to different clusters based on cell compartment (CC), biological process (BP), and molecular function (MF). OA, osteoarthritis; RA, rheumatoid arthritis.