Caenorhabditis elegans L4 N-glycans across culture and release fractions

All 202 molecular-feature rows of Supplementary Table S1, with relative percentages reported for four L4 culture and glycan-release fraction profiles.

Usage

glyhub_GPST000294_N_Celegans_L4(
  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 202 features and 4 observations. The abundance assay is in reported relative percentage. rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000294. Supplementary Table S1, PDF pages 4–17. Study: https://doi.org/10.1016/j.mcpro.2023.100505. Repository: https://glycopost.glycosmos.org/entry/GPST000294.

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

L4 larvae were grown in liquid or on plates. PNGase F and the subsequent Ar release fractions are separate analytical fractions of these preparations, not four independent biological replicates. The table reports percentages for the second L4 preparations together with retention times from eleven preparations. Only the percentage tokens are used in the abundance assay; embryo and first-preparation retention times are preserved as source annotations. All 202 source rows remain, including 14 with no percentage in any profile. There are 147 exact percentage measurements and 150 source values explicitly reported as >0.1%; censored values have missing numeric abundance and retain their literal inequalities. Unreported percentages remain missing. No threshold substitution or renormalization is performed.

Each source diagram is transcribed with its displayed topology and residue identity. Unlabelled glycosidic configurations and acceptor positions remain unknown. Explicit author GlyTouCan accessions refine bond information only after residue-labelled topology is verified. PC and methyl substituents retain their source placement uncertainty, including a PC restricted to two candidate GlcNAc residues. Source composition/mass, original table cells, diagram row and review evidence remain available. All 202 rows have parsed, source-backed structures; broad source H/N/F/substituent totals match where a printed composition exists (201 rows). The one row without printed composition is assigned from its diagram. Twelve explicit GlyTouCan identifiers have residue-labelled topology verification. Row 196 uses the article Results identification of Figure 4I as a branched Man-HexNAc motif to constrain both fragments to the upper-arm Man; row 197 retains uncertain arm placement of long and short chains.

Access

Use glyhub_load("glyhub_GPST000294_N_Celegans_L4") to load this dataset.