GH20 activity on N-glycans from pretreated PSGL-1 and related study experiments

The N-glycan fraction reported alongside the PSGL-1 GH20 enzyme screen. These measurements describe three N-glycan features with exposed N-acetylglucosamine in the pretreated glycoprotein preparation, permitting inspection of enzyme responses outside the O-glycan core panel. Supplementary Table S10B reports the three features across eight conditions. Combined N-glycan quantitative profiles from GPST000643. 3 union features and 23 source observations are represented.

Usage

glyhub_GPST000643_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 3 features and 23 observations. The abundance assay is in percentage of source total glycan AUC. rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000643. Supplementary Table S10B, N-glycan rows 25-27 (media-11.xlsx). Study: https://doi.org/10.64898/2026.03.26.714468. Repository: https://glycopost.glycosmos.org/entry/GPST000643.

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: source-reported percentage of total glycan AUC.

GH20 activity on N-glycans from pretreated PSGL-1: The protein substrate was pretreated with BT0455 sialidase and the galactosidases BT1626 and BT4241 to expose terminal N-acetylglucosamine. The eight conditions are control, BT1621, BT1627, BT3178, BT3598, BT3868, BT4394 and BT4681. There is one source column per condition; biological replicate type and expression-system species are not established by these table columns.

This object follows the workbook's explicit N-glycan classification rather than combining these features with its O-glycan section. It is not a separate set of eight biological samples inferred from that split. The source percentages are preserved without changing their denominator. Compare glyhub_GPST000643_O_S10B for the complementary feature space.

Replicated GH20 measurements of PSGL-1 N-glycan features: The conditions are control, BT3178, BT3598, BT3868 and BT4681, each with Sample 1, Sample 2 and Sample 3. PSGL-1 expressing core 4 was pretreated with an enzyme mix. The expression-system species and biological versus technical replicate type are not established by these table columns. Percentages retain the source total-AUC denominator without renormalization after separation by glycan class.

Mass-labelled features 1317-1 and 1520 are source rows 11 and 12. Their compositions and complete putative-structure text are identical to S10B rows 25 and 26, located under its explicit N-glycans heading. This source correspondence supports the N classification independently of mass alone. The companion glyhub_GPST000643_O_S10C object contains the other three rows; the matrices share their observation identities and must not be counted as separate samples.

The three composition labels and putative structures are encoded, including the source reduced reducing ends.

Access

Use glyhub_load("glyhub_GPST000643_N") to load this dataset.