Oral tumor N-glycans associated with lymph node metastasis

Relative abundances of 83 isomer-resolved N-glycan features from 31 oral squamous cell carcinoma tumors with or without lymph node metastasis.

Usage

glyhub_GPST000296_N(
  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 83 features and 31 observations. The abundance assay is in relative abundance fraction. rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000296. Deposited Glycan_results.xlsx, TS3; published supplementary spectral atlas. Study: https://doi.org/10.1016/j.mcpro.2023.100586. Repository: https://glycopost.glycosmos.org/entry/GPST000296.

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

The complete source matrix contains 12 N0 and 19 N+ tumor samples. Glycan isomers remain distinct and source MS/MS confirmation, retention time, core fucosylation, bisecting GlcNAc and sialic-acid diagnostics are retained. Eighty-two partial structures combine the source spectral atlas with explicit sialic-acid linkage information from Table S3; unnumbered linkages and unresolved arms remain unknown. Feature 9b has no MS/MS-confirmed topology and retains composition only. Analytes were reduced glycans; this preparation is recorded separately from monosaccharide identity.

Source spectral-atlas topologies with TS3-supported sialic linkages; unnumbered linkages and uncertain arms retained as unknown. Composition-only annotation for 9b.

Access

Use glyhub_load("glyhub_GPST000296_N") to load this dataset.