Linkage-specific sialic-acid derivatization of plasma N-glycans

Background-subtracted extracted-ion intensities of procainamide-labelled plasma N-glycans after linkage-specific sialic-acid derivatization.

Usage

glyhub_GPST000190_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 78 features and 54 observations. The abundance assay is in background-subtracted extracted-ion intensity. rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000190. Table S-3. Study: https://doi.org/10.1021/acs.analchem.1c02610. Repository: https://glycopost.glycosmos.org/entry/GPST000190.

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 deposited complete extraction table contains 39 composition/retention features in two charge states across 54 LC-MS runs, including explicitly labelled blanks. Charge states remain separate measurement features rather than being summed without an author-defined rule. Am and E denote the source derivatization products used to distinguish alpha2,3- and alpha2,6-linked sialic acids; their counts are retained alongside the underlying Neu5Ac composition. Unmeasured charge states and reported zeros are missing in the curated assay. Run identifiers retain the original experimental batches; they are not interpreted as independent biological donors.

Composition-level glycans with source charge, retention time, procainamide label, and linkage-specific sialic-acid derivative counts; no full topology inferred.

Access

Use glyhub_load("glyhub_GPST000190_N") to load this dataset.