Atlantic salmon epithelial mucin O-glycans

O-glycan relative abundances from Atlantic salmon skin, pyloric caeca and distal-intestinal mucins across six geographic and husbandry cohorts from Tasmania, Sweden and Norway.

Usage

glyhub_GPST000009_O(
  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 169 features and 57 observations. The abundance assay is in relative abundance (%). rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000009. Sheet1. Study: https://doi.org/10.1074/mcp.ra119.001319. Repository: https://glycopost.glycosmos.org/entry/GPST000009.

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

All compatible tissue and cohort measurements are retained in one matrix. Original retention times, peak areas, suggested structures and per-sample MS1-only asterisks remain available in source annotations. Relative abundance is preserved as reported; ionisation differences limit interpretation across different glycan species. Typed structures describe native residue topology with analytical reducing-end reduction documented separately. Unresolved linkages remain unknown; malformed or sulfated structure strings remain as source annotations pending unambiguous representation.

Source-derived compositions and original labels are retained. 152 source-supported structures are typed; unspecified bonds remain unknown. Unresolved or conflicting structures remain missing with source provenance.

Access

Use glyhub_load("glyhub_GPST000009_O") to load this dataset.