Table 2 Overview of the performance tests applied to establish the relative team performance for glycopeptide data analysis

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

Performance tests

Description of scoring method

N-glycopeptide performance tests

N1

Synthetic N-glycopeptide

Identification accuracy (specificity, %) multiplied by coverage (sensitivity, %) of a synthetic N-glycopeptide (Supplementary Table 5)

N2

N-glycan compositiona

Pearson correlation (R2) between the expected23 and observed N-glycan distribution in human serum (Supplementary Table 6)

N3

Source N-glycoproteina

Specificity and sensitivity of reported source N-glycoproteins relative to expected serum glycoproteins23,39, (Supplementary Table 7)

N4

N-glycoproteome coverage

Unique N-glycopeptides reported (unique peptide sequence and N-glycan composition) (Supplementary Table 8)

N5

Commonly reported ‘consensus’ N-glycopeptides

Proportion of reported N-glycopeptides of the consensus N-glycopeptides commonly reported by >50% of teams (Supplementary Table 9)

N6

NeuGc and multi-Fuc N-glycopeptides (absence)

Proportion of reported N-glycoPSMs not containing NeuGc and multi-Fuc of all reported N-glycoPSMs. Only applicable if NeuGc/multi-Fuc glycans were included in N-glycan search space (Supplementary Table 10)

O-glycopeptide performance tests

O1

O-glycan compositiona

Pearson correlation (R2) between the expected40 and observed O-glycan distribution in human serum (Supplementary Table 11)

O2

Source O-glycoproteina

Specificity and sensitivity of reported source O-glycoproteins relative to expected serum glycoproteins4,41,42, (Supplementary Table 12)

O3

O-glycoproteome coverage

Unique O-glycopeptides reported (unique peptide sequence and O-glycan composition) (Supplementary Table 13)

O4

Commonly reported ‘consensus’ O-glycopeptides

Proportion of reported O-glycopeptides of the consensus O-glycopeptides commonly reported by >30% of teams (Supplementary Table 14)

O5

NeuGc and multi-Fuc O-glycopeptides (absence)

Proportion of reported O-glycoPSMs not containing NeuGc and multi-Fuc of all reported O-glycoPSMs. Only applicable if NeuGc/multi-Fuc glycans were included in O-glycan search space (Supplementary Table 15)

  1. The performance tests scored each team using normalized quantitative values (range 0–1). aSome tests were based on matches to data from robust literature on human serum glycosylation4,23,39,40,41,42. Glycopeptide data from Files A and B showed excellent agreement to the literature (Extended Data Fig. 4).
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