import_maxquant_peptides: Import a label-free proteomics dataset from MaxQuant, using...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Import a label-free proteomics dataset from MaxQuant, using the peptides.txt file

Description

Recommended to import directly from the evidence file using import_dataset_maxquant_evidencetxt instead, as the peptides.txt file lacks retention-tine information !

Usage

import_maxquant_peptides(
  file_peptides,
  remove_shared_peptides = T,
  pep2prot = NA
)

Arguments

file_peptides	full file path to MaxQuant's peptides.txt output file
remove_shared_peptides	remove all peptides that are assigned to multiple proteingroups (checked by having a semicolon in the 'Protein group IDs' column)
pep2prot	if available, provide a 2 column table that provides a mapping from each peptide to a protein. Required columns; protein_id and sequence_plain. Set NA to use "Leading razor protein" as protein grouping

Details

Provided mostly for compatability with incomplete datasets that lack the evidence.txt and proteinGroups.txt files

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