Site-resolved O-glycoform proportions during influenza infection of A549 cells

Complete source O-site glycoforms from Supplementary File 5: union of ten organelle/secreted fraction panels at 0,6,12,18,24 hours after mock, PR8(H1N1), or x31(H3N2) exposure. 253 protein/site/glycan identities across 90 biological sample observations.

Usage

glyhub_GPST000671_O_Glycoproteomics(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Format

A glyexp::GlycoproteomicSE with 253 features and 90 observations. The abundance assay is in site-normalized glycoform proportion (fraction). rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000671. . Study: https://doi.org/10.1038/s42003-026-10759-y. Repository: https://glycopost.glycosmos.org/entry/GPST000671. Quantitative source: https://www.nature.com/articles/s42003-026-10759-y.

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

Assay values are author site-normalized proportions F:N, not raw signal or whole-sample glycan abundance. All source rows assigned to this glycan class are retained. Features are aligned only by the exact Protein/site/Glycans triplet; source Concat was checked to match this triplet in every row. No within-panel duplicate triplets occur. Union cells for a feature absent from a source panel remain NA with source_coverage=false; source blanks and actual zeros remain separately recoverable. Only quantitative zeros become NA. No curation-stage imputation, renormalization or replicate averaging occurs. O:W raw intensities are preserved in columns O:W of the pinned source extraction and original workbook. The three biological replicates per condition follow the paper; replicate numbers 1:3 encode within-condition source-column order, not demonstrated longitudinal pairing across time or compartment. TMT channels are preserved because assignments change with time. Human, bovine and influenza-virus protein assignments are all retained exactly; the culture host is human A549, but row-level protein organism must be used for protein provenance. Released glycomics is a separate assay/object class.

Counts are parsed only from explicit author Glycans tokens. HexNAc, Hex, Fuc and NeuAc are preserved; explicit Phospho and Sulfo are retained as P and S substituents. Protein accession and site positions are author assignments, not independently revalidated peptide localization. All observed source sites are single N/S/T positions; ambiguous or multiple source sites would remain untyped. Full glycan structures are not inferred from composition or site.

Access

Use glyhub_load("glyhub_GPST000671_O_Glycoproteomics") to load this dataset.