import_dataset_encyclopedia: Import a label-free proteomics dataset from EncyclopeDIA

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Import a label-free proteomics dataset from EncyclopeDIA

Description

This function imports peptide intensities, retention times and peptide-to-protein mappings from a 'Quant Report' .elib file generated by EncyclopeDIA.

Usage

import_dataset_encyclopedia(
  file_quant_report,
  path_elib_rawfiles = NA,
  confidence_threshold = 0.01,
  return_decoys = FALSE
)

Arguments

file_quant_report	the EncyclopeDIA 'Quant Report' .elib file
path_elib_rawfiles	optional. the directory that contains the EncyclopeDIA .elib files matching each sample (mzML/dia input file to EncyclopeDIA)
confidence_threshold	confidence score threshold at which a peptide is considered 'identified' (target value must be lesser than or equals)
return_decoys	logical indicating whether to return decoy peptides. It doesn't work for current EncyclopeDIA datasets as these do not seem to contain decoys.

Details

Because this 'Quant Report' does not contain confidence scores per peptide per individual sample, these can optionally be imported from the individual .elib files generated by EncyclopeDIA while processing the individual samples / raw files. This will enable MS-DAP to discriminate between match-between-runs hits and peptides that were detected/identified in a sample, and consequently use this information in peptide filtering (for instance by removing peptides that are mostly based on MBR hits).

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.