Requirements

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)