Immunoglobulins N-glycan total peak areas and related study experiments

N-glycopedia applies structure-specific SRM profiling to purified human immunoglobulins. All 35 rows of the source IgA/IgG/IgM table and nine technical preparation/LC-MS replicate measurements are retained as raw total peak areas; normalized abundances and statistical summaries remain in the source workbook. Combined N-glycan quantitative profiles from GPST000578. 75 union features and 27 source observations are represented.

Usage

glyhub_GPST000578_N_total_peak_area(
  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 75 features and 27 observations. The abundance assay is in total peak area. rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000578. Figure 5bc. Study: https://doi.org/10.1038/s41467-026-73091-3. Repository: https://glycopost.glycosmos.org/entry/GPST000578. Quantitative source: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41467-026-73091-3/MediaObjects/41467_2026_73091_MOESM4_ESM.xls.

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

Source experiments are identified in colData and original panel-specific metadata, annotations and measurements are retained in metadata. Feature identities are aligned only when supported by author identifiers or explicit molecular structures; other features retain source-specific identities. The source_coverage matrix distinguishes unmeasured combinations from measured missing values. Units: total peak area.

Immunoglobulins N-glycan total peak areas: Entire source feature block retained. Zero-valued abundance is to be converted to NA with original values retained; no sample pairing inferred. GlyTouCan IDs are source annotations; sequence/composition mapping is pending verification. Quantitative zeros are represented as NA without imputation or renormalization; original measurements are retained. GlyTouCan identifiers remain the source assignments.

CHO Perturbation N-glycan total peak areas: Entire source feature block retained. Zero-valued abundance is to be converted to NA with original values retained; no sample pairing inferred. GlyTouCan IDs are source annotations; sequence/composition mapping is pending verification. Quantitative zeros are represented as NA without imputation or renormalization; original measurements are retained. GlyTouCan identifiers remain the source assignments.

Recombinant Spike N-glycans from SF9 and CHO expression: Complete 61-feature raw total-area block from Figure 5a. The later 9-feature SF9 and 51-feature CHO presentation blocks repeat measurements from this block; these filtered presentations are retained as source context and not counted as additional observations. Quantitative zeros are represented as NA without imputation or renormalization; original measurements are retained. GlyTouCan identifiers remain the source assignments.

Recombinant Spike N-glycans from HEK293 expression: Complete 34-feature HEK293 source block from Figure 5a, retaining raw total peak areas for the three technical preparations. Source per-glycan class and summary relative values are contextual annotations, not additional samples. Quantitative zeros are represented as NA without imputation or renormalization; original measurements are retained. GlyTouCan identifiers remain the source assignments.

All source GlyTouCan identifiers resolve to WURCS through the official GlyTouCan SPARQL service. Structures are converted with glyparse 0.8.1 and validated with glyrepr 1.1.0, and compositions are derived from the validated structures. No mass-based assignments or new experimental linkage evidence are inferred.

Access

Use glyhub_load("glyhub_GPST000578_N_total_peak_area") to load this dataset.