Fucosidase treatment of porcine colonic mucin O-glycans and related study experiments

LC-MS profiles of porcine colonic mucin oligosaccharides exposed to individual Bacteroides thetaiotaomicron fucosidases. This experiment compares the effects of GH95 and GH29 enzymes on a complex O-glycan substrate containing different fucosylated epitopes. Supplementary Table S5 provides 108 features and 22 observations. Combined O-glycan quantitative profiles from GPST000643. 365 union features and 71 source observations are represented.

Usage

glyhub_GPST000643_O(
  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 365 features and 71 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 S5 (media-6.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.

Fucosidase treatment of porcine colonic mucin O-glycans: The conditions are a no-enzyme control and BT1777, BT3155, BT3173, BT1842, BT3665, BT1625, BT4136, BT3798, BT3956 and BT4713. Each condition has columns labelled Replicate 1 and Replicate 2; these labels alone do not identify biological versus technical replicates.

The source supplies glycan AUCs, retention times and percentages normalized to total glycan AUC per observation. The abundance assay uses the percentages. Fucose, sulfation and blood-group annotations are retained as source annotations, including their zero-valued categorical flags. Features include substrate glycans and enzymatic products; O-derived denotes their experimental origin.

GH89 treatment of porcine gastric mucin O-glycans: The no-enzyme control, BT0438 treatment and BT4359 treatment each have two source-labelled replicates. The assay contains total-AUC-normalized percentages; original AUC and retention-time entries are retained separately in metadata.

Source row 46 has a disagreement between its reported composition and putative structure residue counts. Rows 69 and 70 contain the unresolved composition token HexHAc, so their typed compositions are NA. Original labels and the annotation_consistency field identify these cases. Their quantitative measurements are retained; uncertain molecular assignments should be considered before feature-level interpretation.

GH2 treatment of bovine submaxillary mucin O-glycans: The seven source columns represent a control and separate treatments with BT1626, BT3179, BT3340, BT4050, BT4241 and BT4684. No replicate labels are supplied for these columns. This table concerns bovine submaxillary mucin without the sialidase/fucosidase pretreatment used in the separate S9C experiment.

Abundances are percentages of total source glycan AUC. Source galactose, sialylation, sulfate and fucose annotations accompany the molecular labels. A single column per condition should not be interpreted as replicated evidence for treatment effects.

GH20 activity on O-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.

Only the source O-glycan section is included here. Its N-glycan section is available as glyhub_GPST000643_N_S10B. Percentages retain the denominator supplied in the workbook; separating the sections does not renormalize either matrix. Source mass/isomer labels are local to the table and are not universal glycan identifiers.

Replicated GH20 measurements of PSGL-1 O-glycan core 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.

The retained mass-labelled features are 425-2, 628 and 716 (source rows 8-10). Their composition and full putative-structure labels match the explicitly labelled O-glycan section of S10B. The two N-glycan features from S10C are available in glyhub_GPST000643_N_S10C. Both objects describe the same observation columns; they are complementary feature partitions, not separate biological samples.

Colonic mucin O-glycan degradation by enzyme mixtures: Three source-labelled samples are reported for each of a no-enzyme control, an eleven-enzyme mixture and the same mixture supplemented with BT3868. The base mixture contains BT0455, BT4243, BT1625, BT3173, BT1636, BT1624, BT1626, BT4241, BT1628, BT4681 and BT0438. This is the S11B mixture; it does not include the additional BT4394 used in the distinct S11C experiment.

Measurements are percentages of source total glycan AUC. O-derived features include remaining substrate glycans and released enzymatic products. Sample 1-3 labels are retained without assigning a biological replicate type or pairing the conditions.

Gastric mucin oligosaccharides remaining after bacterial growth: The source conditions are Control (gMO), the double alpha-1,2-fucosidase deletion strain lacking bt3173 and bt4682, that double deletion with an additional bt1842 deletion, and wild-type B. thetaiotaomicron. These are culture-supernatant glycan profiles, not bacterial counts or gene-expression measurements. One percentage column is available for each condition; no biological replicate type is assigned.

Percentages are normalized to source total glycan AUC. Feature row 48 has conflicting composition and putative-structure residue counts; both source assignments are retained and flagged in annotation_consistency. Digestion products and residual substrate glycans should be interpreted together in this extracellular measurement space.

All 108 source composition labels are retained as typed compositions. Forty-seven source putative structures have explicit encodings; remaining structural descriptions are preserved as text without completing unspecified linkages.

Access

Use glyhub_load("glyhub_GPST000643_O") to load this dataset.