Desialylated haptoglobin released N-glycans in sepsis serum

Haptoglobin purified from healthy-control and sepsis serum was analyzed by LC-ESI MS after desialylation. The complete source feature matrix contains three HC0, three SG1 and three SG2 observations.

Usage

glyhub_GPST000533_N_Released(
  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 13 features and 9 observations. The abundance assay is in LC-MS extracted-ion peak intensity. rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000533. results of 231208_Hpt_glycans. Study: https://doi.org/10.1038/s41467-025-56524-3. Repository: https://glycopost.glycosmos.org/entry/GPST000533. Quantitative source: https://glycopost.glycosmos.org/data/GPST000533.0/Result%20file%20of%20231208_Hpt_aTMT6glycans%20for%20Fig%20and%20GlycoPOST.xlsx. Annotation evidence: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41467-025-56524-3/MediaObjects/41467_2025_56524_MOESM1_ESM.pdf.

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

PNGase F-released glycans were labeled with aminoxy tandem mass tag (aTMT6); distinct core- and Lewis-fucosylated chromatographic labels remain separate. Source intensity is the assay; author percentages are preserved separately. No normalization, replicate pooling or composition-from-mass reconstruction is applied. Antennarity and fucosylation labels are mapped to the explicit source SNFG residue counts.

Composition counts are transcribed from the author-labelled SNFG structures in Supplementary Figures 1d/e and 2a. Typed structures preserve unknown linkages; terminal or otherwise unlocalized fucose is left structurally unassigned. Original labels and figure evidence are retained.

Access

Use glyhub_load("glyhub_GPST000533_N_Released") to load this dataset.