Released O-glycans of recombinant SARS-CoV-2 Spike and ACE2

The study characterizes the glycosylation of recombinant Spike and soluble human ACE2. This complete source O-glycan table reports percent of total profile for 16 glycan features in each protein preparation. Columns are protein-level profiles, not biological replicates.

Usage

glyhub_GPST000120_O_Spike_ACE2(
  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 16 features and 2 observations. The abundance assay is in percent of total O-glycan profile. rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000120. Sheet1. Study: https://doi.org/10.1016/j.chom.2020.08.004. Repository: https://glycopost.glycosmos.org/entry/GPST000120. Quantitative source: https://glycopost.glycosmos.org/data/GPST000120.0/olinked3.xlsx. Annotation evidence: https://ts.glytoucan.org/sparql.

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 entire 16-feature source O-glycan table is retained. The two columns are protein-level profiles for recombinant Spike and soluble human ACE2, with no biological replicate identity inferred. Original nd/nd* markers and measurements are retained; abundance zeros and not-detected entries are represented as NA without renormalization.

All 16 source GlyTouCan accessions were resolved to WURCS records from the official GlyTouCan SPARQL service. The registered structures were converted with glyparse 0.8.1, reparsed and validated with glyrepr 1.1.0, and compositions derived from those structures. This preserves the source accession assignments and does not infer structures from mass or infer new experimental linkage evidence.

Access

Use glyhub_load("glyhub_GPST000120_O_Spike_ACE2") to load this dataset.