import_dataset_skyline: Import a label-free proteomics dataset from Skyline

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Import a label-free proteomics dataset from Skyline

Description

Import a label-free proteomics dataset from Skyline

Usage

import_dataset_skyline(
  filename,
  acquisition_mode,
  confidence_threshold = 0.01,
  collapse_peptide_by = "sequence_modified",
  return_decoys = FALSE,
  do_plot = TRUE
)

Arguments

filename	the full file path of the input file
acquisition_mode	the type of experiment, should be a string. options: "dda" or "dia"
confidence_threshold	confidence score threshold at which a peptide is considered 'identified', default: 0.01 (target value must be lesser than or equals)
collapse_peptide_by	FOR DDA ONLY (acquisition_mode='dda'): if multiple data points are available for a peptide in a sample, at what level should these be combined? options: "sequence_modified" (recommended default), "sequence_plain", ""
return_decoys	logical indicating whether to return decoy peptides. Should be set to FALSE, and if enabled, make sure to manually remove the decoys from the peptides tibble before running the quickstart function!
do_plot	logical indicating whether to create QC plots that are shown in the downstream PDF report (if enabled)

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