Import

In mpwR: Standardized Comparison of Workflows in Mass Spectrometry-Based Bottom-Up Proteomics

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Introduction

This vignette gives an overview about importing files for downstream analysis with mpwR.

Import

Importing the output files from each software can be easily performed with prepare_mpwR. Please put all output files in one folder and follow the guidelines for naming the files. No other files/subfolders are allowed.

files <- prepare_mpwR(path = "Path_to_Folder_with_files")

Naming Files

The software output files need to be named according some simple rules.

Suffix

Please use the following suffixes for the corresponding software:

• Spectronaut

  • *.tsv - _Report

• MaxQuant

  • evidence.txt - _evidence
  • peptides.txt - _peptides
  • proteinGroups.txt - _proteinGroups

• DIA-NN

  • *.tsv - _Report

• ProteomeDiscoverer

  • PSMs.txt - _PSMs
  • PeptideGroups.txt - _PeptideGroups
  • Proteins.txt - _Proteins
  • ProteinGroups.txt - _ProteinGroups

Note that the suffixes for MaxQuant and ProteomeDiscoverer can be used as is.

Prefix

Please use the same prefix for your analysis and the respective software output file(s). Each analysis needs a unique identifier.

Examples:

• Spectronaut

  • WorkflowA1_Report.tsv

• MaxQuant

  • WorkflowA2_evidence.txt
  • WorkflowA2_peptide.txt
  • WorkflowA2_proteinGroups.txt

• DIA-NN

  • WorkflowA3_Report.tsv

• ProteomeDiscoverer

  • WorkflowA4_PSMs.txt
  • WorkflowA4_PeptideGroups.txt
  • WorkflowA4_Proteins.txt
  • WorkflowA4_ProteinGroups.txt

Handling Error Messages

Subsequently, common error messages are explained and solutions are pointed out.

 

 

Wrong suffix

Error in prepare_mpwR(path = path) : Unknown file suffix detected! Please use: _evidence, _peptides, _proteinGroups, _PSMs, _Proteins, _PeptideGroups, _ProteinGroups, _Report

 

Solution: Check your suffixes and make sure to use the correct spelling and the correct one for the respective software.

 

 

Wrong number of files

Error in prepare_mpwR(path = path) : Wrong number of analyses detected for WorkflowA2! MaxQuant requires 3 input files. Remember: Use unique name for each analysis.

 

Solution: Make sure to include all output files from the respective software. MaxQuant requires 3 files, PD 4 files, DIA-NN and Spectronaut 1 file, respectively. Also use the same name (prefix) for all files.

 

 

Subfolder

Error in data.table::fread(input_file, ...) : File 'DIR//subfolder' is a directory. Not yet implemented.

 

Solution: Do not use subfolders in the directory of the output files. Put all files in a folder and use this path for prepare_mpwR.

 

 

Same file name

Error in prepare_mpwR(path = path) : Please use a unique filename for each analysis.

 

Solution: Please use a unique name (prefix) for each respective output file(s). E.g. if you used...:

• WorkflowA1_Report.tsv
• WorkflowA1_evidence.txt
• WorkflowA1_peptide.txt
• WorkflowA1_proteinGroups.txt

... the error message is displayed. As a solution, for example add the used software to the name:

• WorkflowA1_Spectronaut_Report.tsv
• WorkflowA1_MQ_evidence.txt
• WorkflowA1_MQ_peptide.txt
• WorkflowA1_MQ_proteinGroups.txt

 

 

Missing columns

Error in prepare_input(ordered_files[[i]][["data"]][["DIA-NN"]], software = "DIA-NN") : Not all required columns present in submitted data.

Here example for DIA-NN. Similar messages for other software tools. Please make sure to include all required columns for the used software. Details are in the vignette Requirements.

mpwR documentation built on June 8, 2025, 10:47 a.m.