Read pGlyco3-pGlycoQuant result

If you used pGlyco3 for intact glycopeptide identification, and used pGlycoQuant for quantification, this is the function for you. It reads in a pGlycoQuant result file and returns a glyexp::experiment() object. Currently only label-free quantification is supported.

Usage

read_pglyco3_pglycoquant(
  fp,
  sample_info = NULL,
  quant_method = c("label-free", "TMT"),
  glycan_type = c("N", "O"),
  sample_name_converter = NULL
)

Arguments

fp: File path of the pGlyco3 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. Either "N" or "O". 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.

Value

An glyexp::experiment() object.

Which file to use?

You should use the "Quant.spectra.list" file in the pGlycoQuant result folder. Files from pGlyco3 result folder are not needed. For instructions on how to use pGlyco3 and pGlycoQuant, please refer to the manual: pGlycoQuant.

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 RawName column in the pGlyco3 result file, although the order can be different.

You can put any useful information in the sample information file. Recommended columns are:

group: grouping or conditions, e.g. "control" or "tumor", required for most downstream analyses
batch: batch information, required for batch effect correction

Output

This function returns a glyexp::experiment() object.

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

charge: integer, charge state
peptide: character, peptide sequence
modifications: character, modifications other than glycosylation, separated by semicolon, e.g. 5,Carbamidomethyl[C];10,Carbamidomethyl[C]
glycan_composition: glyrepr::glycan_composition(), glycan compositions.
glycan_structure: glyrepr::glycan_structure(), glycan structures.
peptide_site: integer, site of glycosylation on peptide
proteins: character, protein names, separated by semicolon
genes: character, gene names, separated by semicolon
protein_sites: character, site of glycosylation on protein, separated by semicolon