Table 1.
Overview of important study variables including key search settings (SS1–SS13) and search output (SO1–SO9)
| Search settings | Typea | Range or definition of category (team count) | |
| SS1 | N-glycan search space | Num | 23–381 unique N-glycan compositions |
| SS2 | O-glycan search space | Num | 3–223 unique O-glycan compositions |
| SS3 | Search engine(s) applied | Cat | Byonic (11), Protein Prospector (2), GlycoPAT (1), GlycopeptideGraphMS (1), glyXtoolMS (1), GPQuest (1), other (5) |
| SS4 | Type of search engine | Cat | Academic/open access/in-house = 0 (7), commercial = 1 (15) |
| SS5 | Spectral calibration postacquisition | Cat | No = 0 (18), Yes = 1 (4) |
| SS6 | Protease specificity | Cat | Nontryptic (N- or C-ragged or nonspecific) = 0 (8), tryptic = −1 (14) |
| SS7 | Missed peptide cleavages permitted | Num | 0–2 missed cleavages |
| SS8 | Variable peptide modification(s) (nonglycan) | Num | 0–14 nonglycan modification types |
| SS9 | Maximum glycans per peptide | Num | 1–5 glycans/peptide |
| SS10 | Maximum other variable modifications | Num | 0–5 variable modifications/peptide |
| SS11 | Precursor ion mass error permitted | Cat | Low (<5 ppm) = 0 (6), medium (5–10 ppm) = 1 (14), high (>10 ppm) = 2 (2) |
| SS12 | Product ion mass error permitted | Cat | Low (<5 ppm) = 0 (0), medium (5–10 ppm) = 1 (9), high (>10 ppm) = 2 (13) |
| SS13 | Peptide/protein FDR (decoy/contaminant database) | Cat | No decoy/contaminant = 0 (3), only decoy or contaminant = 1 (9), both decoy and contaminant = 2 (10) |
| Search output | Typea | Range | |
| (N- or O-glycosylation) | |||
| SO1 | Glycopeptide LC retention timeb | Num | 41.7–57.2 min (NG) |
| 26.2–55.8 min (OG) | |||
| SO2 | Glycopeptide m/z (observed)b | Num | m/z 712.9–1199.4 (NG) |
| m/z 619.6–1229.0 (OG) | |||
| SO3 | Glycopeptide charge state (observed)b | Num | z = 3.9–4.3 (NG) |
| z = 3.1–5.4 (OG) | |||
| SO4 | Monoisotopic correction (off-by-X, positive values)b | Num | 0–2.1 Da (NG) |
| 0–2.0 Da (OG) | |||
| SO5 | Glycopeptide mass ([M + H]+, observed)b | Num | 3144.6–4913.0 Da (NG) |
| 1892.9–6057.1 Da (OG) | |||
| SO6 | Glycopeptide actual mass error (observed, positive values)b | Num | 0.5–2.8 ppm (NG) |
| 1.1–5.9 ppm (OG) | |||
| SO7 | Glycopeptide lengthb | Num | 16.9–26.8 AA (NG) |
| 14.5–38.9 AA (OG) | |||
| SO8 | Glycan mass (calculated from reported glycopeptides)b | Num | 1880.8–2410.1 Da (NG) |
| 195.8–2216.8 Da (OG) | |||
| SO9 | Reported glycoPSMs | Num | 49–2122 glycoPSMs (NG) |
| 5–578 glycoPSMs (OG) | |||
See Supplementary Tables 1–4 for details. aNum, numerical variable; Cat, categorical variable. NG, N-glycosylation; OG, O-glycosylation. bAverage of output data reported by each team. AA, amino acid residues. While reported glycoPSMs were considered search output (SO9), unique glycopeptides were used to score the glycoproteome coverage (N4, O3).