Desialylated haptoglobin glycopeptides in sepsis serum

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

Usage

glyhub_GPST000533_N_Glycopeptides(
  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 54 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 231111_Hpt. 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%20231111_Hpt_glycopeptides%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

The source protein is UniProt P00738. All six quantitative panels in the selected author sheet are retained: Site 3 (3+), Site 4 (4+ and 3+), Site 2 (3+ and 2+), and oxidized Site 1 (3+). Charge states are distinct features, not independent samples, and are not summed. All panels have matching sample and raw-data identifiers. Source Site 1 binding position 84 conflicts with the listed peptide interval 179-194, so typed protein_site is NA for that panel. Other site positions are retained directly. 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 source annotations. Compositions and supported structures are transcribed from directly reviewed Supplementary Figures 1d/e and 2a; unresolved fucose positions remain structurally unassigned.

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_Glycopeptides") to load this dataset.