Brugia malayi N-glycans across life stages

MALDI-TOF MS peak-area profiles of released glycans from mixed-sex adult worms, microfilariae, adult females and adult males, and L3 larvae.

Usage

glyhub_GPST000240_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 47 features and 9 observations. The abundance assay is in MALDI-TOF MS integrated peak area (arbitrary units). rowData includes a typed glycan_structure column; features without a supported structure are NA.

Source

GlycoPOST GPST000240. Supplementary Table S3, B - MALDI Raw Data. Study: https://doi.org/10.1016/j.mcpro.2022.100201. Repository: https://glycopost.glycosmos.org/entry/GPST000240.

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

Forty-seven source-assigned molecular features are retained, including features without a quantified assignment in a particular spectrum. Mixed-sex adult and microfilarial material each have an original spectrum and two explicitly labelled biological replicates. Sex-separated adults and L3 larvae have one profile each. Areas are preserved on the source instrumental scale. Unassigned or undetected features remain missing; no zero filling or normalization is applied. Source phosphorylcholine and glucuronic-acid composition components are represented explicitly. Proposed structural diagrams are transcribed and composition-checked against the same source feature rows. Unlabelled bonds are unknown; source ambiguity braces are represented as floating groups without selecting a particular attachment.

47 proposed source structures are encoded with unspecified linkages and floating groups kept uncertain. Source compositions preserve Hex, HexNAc, Fuc, GlcA and phosphorylcholine; analytical anthranilic-acid labeling is recorded separately.

Access

Use glyhub_load("glyhub_GPST000240_N") to load this dataset.