Mgat3 mouse brain and kidney N-glycan source profiles

Source-preserving study-level N-glycan resource from Mgat3 wild-type and knockout mouse brain and kidney. It contains the complete published 51-feature brain table and 287-feature kidney workbook as distinct source panels.

Usage

glyhub_GPST000027_031_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 338 features and 6 observations. The abundance assay is in source EIC peak intensity (panel-specific instrument units). rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000027 and GPST000031. Supplementary Figure S2C (PDF page 4) and Supplemental Table S2 (WT&Mgat3KO sheet). Study: https://doi.org/10.1074/mcp.RA119.001534. Repository: https://glycopost.glycosmos.org/entry/GPST000027 and https://glycopost.glycosmos.org/entry/GPST000031. Quantitative source: https://pmc.ncbi.nlm.nih.gov/articles/PMC6773561/.

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 object is a disjoint union of 338 source-specific chromatographic features across six source observations: two genotype-labelled brain profiles and four kidney sample/run columns. Of the 2,028 storage cells, 1,250 are measured source cells and 778 cross-panel combinations are unmeasured; source_coverage and processing_masks distinguish these from the 324 source zeros represented as NA. The original brain and kidney matrices, annotations, sample metadata and exact maps remain in metadata(x)$panels, panel_row_data, panel_col_data and panel_maps. No rows are aligned across tissues using composition, mass or author numbering.

The one abundance assay retains EIC peak intensities in panel-specific instrument units. Brain uses aminoxyTMT6 whereas kidney uses aminoxyTMT0; combining storage does not establish calibrated numerical comparability across tissues or protocols. Original percentages remain metadata(x)$source_relative_abundance, not a second assay. Both source percentage blocks use high-mannose intensity sums as denominators rather than total glycome. Brain values retain the published one-decimal precision; kidney values retain Excel precision. No averaging, imputation or normalization is added.

Kidney workbook run IDs exactly match four GPST000031 raw filenames. Brain S2C supplies no run or replicate IDs; its raw-file links are explicitly marked genotype-and-filename-based candidates in GPST000027. Although the article reports three independent brain WT/KO pairs, only two genotype columns are published in S2C; these are not expanded or labelled as independent individual mice. Biological replication, pairing, age and sex are not inferred. This object represents the complete published tables, not every raw detected peak or every experiment in the paper.

306 features have a single source composition, retaining generic residues plus the explicitly stated Man3GlcNAc2 core. For 32 ambiguous kidney features, typed composition is NA while every original candidate string/count and all quantitative cells remain. Chromatographic subpeaks stay distinct even when composition and mass match. Diagnostic MS/MS scan identifiers do not establish complete topology; no glycan_structure column is present. Source file attribution and article-version CC BY 4.0 license evidence are retained separately from the package code license; no supplement-specific license declaration was independently verified.

Access

Use glyhub_load("glyhub_GPST000027_031_N") to load this dataset.