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
- 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
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
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
- Peptide Groups Peptide Group ID
- Confidence
- Sequence
- Modifications
- Number of Missed Cleavages
- Found in Sample column(s)
- Proteins.txt
- Proteins Unique Sequence ID
- Protein FDR Confidence Combined
- Accession
- Description
- Found in Sample column(s)
- ProteinGroups.txt
- Protein Groups Protein Group ID
- Group Description
- Number of Proteins
- Number of Unique Peptides
- Found in Sample column(s)