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)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.