Site-specific N-glycoproteome of oral squamous-cell carcinoma tissues

Quantitative N-glycopeptide profiles of 30 oral squamous-cell carcinoma tumour tissues, comprising 12 node-negative and 18 node-positive samples.

Usage

glyhub_GPST000296_N_Glycoproteomics(
  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 3117 features and 30 observations. The abundance assay is in pooled-reference-normalized and channel-total-normalized reporter-ion abundance (fraction). rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000296. . Study: https://doi.org/10.1016/j.mcpro.2023.100586. Repository: https://glycopost.glycosmos.org/entry/GPST000296. Quantitative source: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10336694/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

The 3,117 author-grouped UniProt, protein-site and glycan-composition features are retained. Reporter ion intensities were divided by the pooled reference channel within each TMT experiment and normalized to each channel total. Source NaN values remain missing; numerical zeros become NA. No reaggregation or imputation is applied. The companion released-glycan dataset has a different molecular observation unit and is retained separately.

Compositions are transcribed directly from the Glycan field. Protein positions come from the author glycopeptide identifier and agree with every reported Glycosite entry. Peptide-relative positions and peptide starts are retained separately; all reported start plus relative-position coordinates agree with the protein absolute position. Representative peptide sequences cannot consistently validate every PSM-relative position, so original fields and a residue-consistency flag are retained without changing the author site. No site-specific glycan topology is inferred from companion released-glycan diagrams.

Access

Use glyhub_load("glyhub_GPST000296_N_Glycoproteomics") to load this dataset.