Extended Data Fig. 9: Comparison of the raw (before normalization) performance scores arising from the glycopeptide identifications based on HCD- or EThcD-MS/MS data. | Nature Methods

Extended Data Fig. 9: Comparison of the raw (before normalization) performance scores arising from the glycopeptide identifications based on HCD- or EThcD-MS/MS data.

From: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis

Extended Data Fig. 9

Only glycopeptides unambiguously reported by either HCD- or EThcD-MS/MS data were included in this analysis. a. N-glycan composition (N2), b. source N-glycoprotein (N3), and c. N-glycoproteome coverage (N4) were calculated using HCD-MS/MS glycoPSMs reported by 17 teams and EThcD-MS/MS glycoPSMs reported by 13 teams. d. O-glycan composition (O2), e. source O-glycoprotein (O2) and f. O-glycoproteome coverage (O3) were calculated using HCD-MS/MS glycoPSMs reported by 16 teams and EThcD-MS/MS glycoPSMs reported by 10 teams. Significance was tested between the HCD- and EThcD-MS/MS data for all performance scores using unpaired two-sided t-tests where ** indicates P = 0.0021.

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