import_dataset_fragpipe_ionquant__legacy: THIS FUNCTION SHOULD ONLY BE USED FOR LEGACY FRAGPIPE...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

THIS FUNCTION SHOULD ONLY BE USED FOR LEGACY FRAGPIPE DATASETS THAT PRODUCED 'mbr_ion.tsv' OUTPUT FILES (e.g. FragPipe v15)

Description

To generate output files that we here require in MS-DAP, configure FragPipe as follows:

• assign Experiment IDs in the workflow tab (you may simply set these all to 1)

• enable IonQuant ("Quant (MS1)" tab, as of FragPipe v15)

• optionally, enable match-between-runs

Usage

import_dataset_fragpipe_ionquant__legacy(
  path,
  acquisition_mode,
  confidence_threshold = 0.01,
  collapse_peptide_by = "sequence_modified"
)

Arguments

path	the full file path to the fragpipe output directory
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' (target value must be lesser than or equals)
collapse_peptide_by	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", ""

Details

This function will merge data from various FragPipe output files to construct a MS-DAP dataset by parsing PSM hits from "psm.tsv" files, collecting IonQuant peptide abundance values from "MSstats.csv" and "mbr_ion.tsv", and finally fetching protein-group information from "combined_protein.tsv".

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