N-glycomes of influenza-infected A549 organelle and secreted fractions

131 released N-glycan chromatographic features in organelle and secreted protein fractions of A549 cells 24 hours after PR8 (H1N1), x31 (H3N2) or mock infection.

Usage

glyhub_GPST000671_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 131 features and 24 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 GPST000671. . Study: https://doi.org/10.1038/s42003-026-10759-y. Repository: https://glycopost.glycosmos.org/entry/GPST000671. Quantitative source: https://glycopost.glycosmos.org/data/GPST000671.0/Supplementary%20File_4_Glycomics.xlsx.

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

PGC-LC-MS/MS glycan abundances are author-normalized proportions of all glycans in each sample. Compatible organelle and secreted fractions are combined with explicit compartment and infection metadata. Four biological replicates per condition were planned. The O-glycan secreted x31 block contains only two observations in the deposited quantitative table; missing observations are not invented. Source isomer identifiers and diagnostic evidence are retained. The deposited N-glycan table contains 131 quantitative features, whereas the publication describes 142 identified N-glycan structures; this object reproduces the available quantitative matrix rather than claiming to include undocumented features. The corresponding molecular feature blocks in official Supplementary Data 4 were checked cell-by-cell and match the deposited workbook.

Source monosaccharide counts and author GlyTouCan accessions are retained. Where an accession resolves to a parseable WURCS structure with composition consistent with the source row, its structure is included. Unresolvable accessions, incompatible compositions and rows without sequence-level structure remain unfilled. Sulfate/phosphate identity is resolved only when the row explicitly names it; ambiguous substitution remains source annotation without a falsely complete composition. Glycans were chemically reduced for measurement; structures represent the source-referenced glycan identity.

Access

Use glyhub_load("glyhub_GPST000671_N") to load this dataset.