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Real glycoproteomics experiment

real_experiment.Rd

A real glycoproteomics experiment object. This dataset is derived from the unpublished ProteomeXchange dataset PXD063749. It contains serum N-glycoproteome profiles from 12 patients with different liver conditions: healthy (H), hepatitis (M), cirrhosis (Y), and hepatocellular carcinoma (C). Glycopeptide identification and annotation were performed using pGlyco3 (https://github.com/pFindStudio/pGlyco3), and quantification was carried out with pGlycoQuant (https://github.com/Power-Quant/pGlycoQuant). The raw data were imported with glyread::read_pglyco3_pglycoquant().

Usage

real_experiment

Format

An experiment() object with 4262 variables and 12 samples.

Variable information:

  • peptide: peptide sequence

  • peptide_site: site position on the peptide

  • protein: protein accession

  • protein_site: site position on the protein

  • gene: gene symbol

  • glycan_composition: glycan composition (glyrepr::glycan_composition())

  • glycan_structure: glycan structure (glyrepr::glycan_structure())

Sample information:

  • sample: sample ID

  • group: disease group, one of "H" (healthy), "M" (hepatitis), "Y" (cirrhosis), and "C" (hepatocellular carcinoma)