# 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)