Caenorhabditis elegans developmental O-glycan profiles

Complete Supplementary Table S2 of Increasing Complexity of the N-Glycome During Caenorhabditis Development: 20 O-glycan features quantified across six source culture profiles.

Usage

glyhub_GPST000294_O_Celegans_Development(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Format

A glyexp::GlycomicSE with 20 features and 6 observations. The abundance assay is in percent occurrence. rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000294. . Study: https://doi.org/10.1016/j.mcpro.2023.100505. Repository: https://glycopost.glycosmos.org/entry/GPST000294. Quantitative source: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7614267/supplementaryFiles.

Arguments

kind: "curated" returns a data object; "raw" returns the path to a verified source archive. Raw archives are currently available for CPTAC.
cache_dir: Cache directory, defaulting to tools::R_user_dir("glyhub", "cache"). Set option glyhub.cache_dir to change the default.
refresh: Download the pinned resource again, even if cached.
offline: Prohibit downloads; require a verified local resource.

Details

O-glycans were released by reductive beta-elimination from peptic glycopeptides remaining after PNGase A/F digestion and analyzed without further derivatization by LC-ESI-MS. Source PDF page 18 has calculated m/z, RT, composition and paired observed-m/z/percentage columns for six samples. Only percentage occurrence is quantitative abundance; observed m/z, nd and fragmentation asterisks are annotations. All 20 rows are retained, including same-composition isomers. Quantitative zeros become NA without imputation or renormalization; raw zeros are preserved. Source columns are culture profiles, not six biological replicates of a common condition. Replication for individual S2 profiles is not explicit and remains unknown. The separately distributed N-glycan Table S1 object extracts the reported percentages from mixed retention-time/percentage cells, preserving censored inequalities and unreported values explicitly.

Explicit author composition tokens provide Hex, HexNAc, dHex, HexA and PC/Me substituent counts. The source Hex3HexNAc1 Hex1Me has four Hex residues and one Me substituent. No Fuc identity is assigned to generic dHex. Linear/branched qualifiers and source isomers remain annotations; no full structure is inferred.

Access

Use glyhub_load("glyhub_GPST000294_O_Celegans_Development") to load this dataset.