Fig. 2: Systematic evaluation of GlyPep-Quant quantification performance.

a Histogram of core-fucoslyated glycopeptides quantitative ratios between the experimental and control groups reported by GlyPep-Quant MBR for glycotransferase gene knockout sample dataset. b, c Histogram of fucosylated (b) and bisecting (c) glycopeptides quantitative ratios between the experimental and control groups reported by GlyPep-Quant based on Glyco-Decipher identification in the exoglycosidase-treatment sample dataset. d Heatmap of quantification values from the two-species proteome dataset. Quantitative values of glycopeptides for proteins that do not belong to the species are considered as entrapment values, which are shown in orange. True positive quantitative values are colored in blue. All quantification values are displayed in log2 scale. e Quantification results of different software tools on the two-species proteome sample. Above box plot: fold-change results of human serum and yeast glycopeptide. Boxes show the median values, which are also labeled near the boxes, and the interquartile ranges. The whiskers are 1.5-fold of interquartile and the outliers are hidden. Theoretical fold changes of organisms in different samples are marked in the figures. Below bar plot: Number of quantified glycopeptides without missing values from different tools. Source data are provided as a Source Data file. f Number comparison of quantification values and quantified glycopeptides between different tools in HeLa cell dataset. Standard deviations of different quantification results are listed in the right. “DB” means the glycopeptides with database glycans; “Modified” means glycopeptides with database glycans and with modified glycans identified by monosaccharide stepping.