Combine Glyco-Decipher GPSM results into a long-format table

Source: R/io_gpsm_import.R

Read multiple Glyco-Decipher GPSM files from a folder, merge them into a unified protein–peptide–glycan table, and attach glycan structures (WURCS 2.0).

read_decipher_gpsm(gpsm_folder_dir)

Arguments

gpsm_folder_dir

The path to a folder containing Glyco-Decipher GPSM files (e.g. files ending with "_GPSM_DatabaseGlycan.txt").

Value

A data frame in long format with one row per Protein–Peptide–GlycanStructure–File combination and the following columns:

  • Protein — protein identifier(s)

  • Peptide — peptide sequence

  • GlycanStructure — glycan structural annotation (WURCS 2.0)

  • File — raw file name

  • Count — spectral count (number of GPSMs) for this combination

Details

This function assumes that the input folder contains one or more Glyco-Decipher GPSM files, typically named with the suffix "_GPSM_DatabaseGlycan.txt". For each file, GPSM records are read and collapsed by Protein, Peptide, GlycanID, File, and Count. All files are then combined into a single table, and glycan IDs are mapped to WURCS structures via the global glycanDatabase object. The final table uses a standardized glycan column name GlycanStructure for compatibility with downstream functions.