Read GlycanFinder result

GlycanFinder is a software for intact glycopeptide identification. This function reads in the result file and returns a glyexp::experiment() object. Currently only label-free quantification is supported.

Usage

read_glycan_finder(
  fp,
  sample_info = NULL,
  quant_method = "label-free",
  glycan_type = "N",
  sample_name_converter = NULL,
  orgdb = "org.Hs.eg.db",
  parse_structure = TRUE
)

Arguments

fp: File path of the GlycanFinder result file.
sample_info: File path of the sample information file (csv), or a sample information data.frame/tibble.
quant_method: Quantification method. Either "label-free" or "TMT".
glycan_type: Glycan type. One of "N", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", or "O-Glc". Default is "N".
sample_name_converter: A function to convert sample names from file paths. The function should take a character vector of old sample names and return new sample names. Note that sample names in sample_info should match the new names. If NULL, original names are kept.
orgdb: Name of the OrgDb package to use for UniProt to gene symbol conversion. Default is "org.Hs.eg.db".
parse_structure: Logical. Whether to parse glycan structures. If TRUE (default), glycan structures are parsed and included in the var_info as glycan_structure column. If FALSE, structure parsing is skipped and structure-related columns are removed.

Value

An glyexp::experiment() object.

Which file to use?

You should use the lfq/lfq.protein-glycopeptides.csv file from the GlycanFinder result folder. This file contains the quantification information for glycopeptides.

Sample information

The sample information file should be a csv file with the first column named sample, and the rest of the columns being sample information. The sample column must match the sample names in the Area columns of the GlycanFinder result file (e.g., "C_3", "H_3"), although the order can be different.

Variable information

The following columns could be found in the variable information tibble:

peptide: character, peptide sequence
peptide_site: integer, site of glycosylation on peptide
protein: character, protein accession
protein_site: integer, site of glycosylation on protein
gene: character, gene name (symbol)
glycan_composition: glyrepr::glycan_composition(), glycan compositions.
glycan_structure: glyrepr::glycan_structure(), glycan structures (if parse_structure = TRUE).