Brugia malayi glycosphingolipid glycans across life stages

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

Usage

glyhub_GPST000240_GSL(
  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 8 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 S4, 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 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. GSL-GP34 has H2N6PC1A1 in the source composition but H2N4PC1A1 in its proposed diagram; both typed composition and structure are missing for this feature, while the conflicting evidence and peak areas remain available.

46 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_GSL") to load this dataset.