import_dataset_spectronaut: Import a label-free proteomics dataset from Spectronaut

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Import a label-free proteomics dataset from Spectronaut

Description

No particular settings are needed, a report with peptide abundances should be made that contains these columns: R.FileName, PG.ProteinGroups, EG.IsDecoy, EG.Library, EG.Qvalue, EG.iRTEmpirical, EG.Cscore, FG.Id, FG.MS2Quantity, FG.MS2RawQuantity

Usage

import_dataset_spectronaut(
  filename,
  confidence_threshold = 0.01,
  use_normalized_intensities = FALSE,
  use_irt = TRUE,
  return_decoys = FALSE,
  remove_shared_spectronaut_proteingroups = FALSE,
  do_plot = TRUE
)

Arguments

filename	the full file path of the input file
confidence_threshold	confidence score threshold at which a peptide is considered 'identified', default: 0.01 (target value must be lesser than or equals)
use_normalized_intensities	use the abundance values as-is (recommended) or those normalized by Spectronaut
use_irt	logical indicating whether to use standardized (IRT, EG.iRTEmpirical) or the empirical (EG.RTEmpirical) retention times
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!
remove_shared_spectronaut_proteingroups	if the peptide-to-proteingroup assignments from Spectronaut are used as is (eg; you're not mapping the peptides to some spectral library downstream), you can remove peptides that map to multiple proteingroups
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.