Requirements

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

knitr::opts_chunk$set(
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Introduction

This vignette gives an overview about requirements for mpwR. The outputs of the following software applications are supported:

• Spectronaut
• MaxQuant
• DIA-NN
• Proteome Discoverer

Spectronaut

The following columns are required:

• R.FileName
• PG.ProteinGroups
• PG.Quantity
• PEP.StrippedSequence
• PEP.NrOfMissedCleavages
• PEP.Quantity
• EG.Identified
• EG.ModifiedPeptide
• EG.PrecursorId
• EG.ApexRT
• FG.Charge

MaxQuant

The following files and respective columns are required:

• evidence.txt

  • Raw file
  • Proteins
  • Sequence
  • Missed cleavages
  • Retention time
  • Modified sequence
  • Charge
  • Protein group IDs
  • Peptide ID
  • Potential contaminant
  • Reverse
  • Intensity

• peptides.txt

  • Sequence
  • Missed cleavages
  • Last amino acid
  • Amino acid after
  • Intensity column(s)
  • LFQ intensity column(s)
  • Protein group IDs
  • Evidence IDs
  • Potential contaminant
  • Reverse

• proteinGroups.txt

  • ProteinIDs
  • Majority protein IDs
  • Peptide counts (all)
  • Intensity column(s)
  • LFQ intensity column(s)
  • id
  • Peptide IDs
  • Evidence IDs
  • Potential contaminant
  • Reverse
  • Only identified by site

DIA-NN

The following columns are required:

• Protein.Group
• Precursor.Id
• Run
• Stripped.Sequence
• Protein.Ids
• Modified.Sequence
• PG.MaxLFQ
• Precursor.Charge
• RT
• Precursor.Id
• Precursor.Quantity
• PG.Q.Value
• Q.Value

Proteome Discoverer

Please enable R-friendly headers for exporting the files. The following files and respective columns are required:

• PSMs.txt

  • Confidence
  • Spectrum File
  • Number of Missed Cleavages
  • Protein Accessions
  • Annotated Sequence
  • Modifications
  • Charge
  • RT in min

• PeptideGroups.txt

  • Number of Protein Groups
  • Number of Proteins
  • Number of PSMs
  • Confidence
  • Sequence
  • Modifications
  • Number of Missed Cleavages
  • Found in Sample column(s) (Required: Data Distributions node in the consensus workflow; set Show Found in Samples parameter to True)

• Proteins.txt

  • Proteins Unique Sequence ID
  • Protein FDR Confidence Combined
  • Accession
  • Description
  • Found in Sample column(s) (Required: Data Distributions node in the consensus workflow; set Show Found in Samples parameter to True)

• ProteinGroups.txt

  • Protein Groups Protein Group ID
  • Group Description
  • Number of Proteins
  • Number of Unique Peptides
  • Found in Sample column(s) (Required: Data Distributions node in the consensus workflow; set Show Found in Samples parameter to True)

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