Fig. 4: Large-scale quantitative analyses of the proteome and N-glycoproteome of different metastatic HCC cell lines with pGlycoQuant.

a Experimental workflow. b The numbers of proteins and intact glycopeptides quantified from proteomic and intact N-glycopeptide quantitation experiments, respectively. The bar in blue represents the number of proteins/glycopeptides quantified in more than two replicates, and the bar in orange represents the number of proteins/glycopeptides quantified in <3 replicates. c General information on 6435 reliably quantified intact N-glycopeptides. Volcano map of differential proteins (d) and intact glycopeptides (e) among three cell lines. Significant differential expression in the volcano plots were calculated by two-sided t-test and the false discovery rate (FDR)-adjusted P-values were calculated by Benjamini–Hochberg (BH) FDR-controlling method for multiple testing. The detailed data are shown in the Supplementary Data 4 and 5. Box diagram with four replicates for the quantitation of proteins (f) and intact glycopeptides (g). In the box plots of f and g, the center line indicates the median. The boxes indicate the interquartile ranges (IQRs), and the whiskers indicate 1.5 × IQR values (with outliers shown). Principal component analysis (PCA) plot of differential proteins (h) and differential intact glycopeptides (i) among three cell lines.