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Requirements

Oliver Kardell

Introduction

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

Spectronaut (v15)
MaxQuant (v2.0.3)
DIA-NN (v1.8)
Proteome Discoverer (v2.4)

Spectronaut

For flowTraceR the following columns are required:

PG.ProteinGroups (User Manual definition: One or several protein groups)
EG.PrecursorId (User Manual definition: Unique Id for the precursor: [modified sequence] plus [charge])

MaxQuant

For flowTraceR the following files and respective columns are required:

evidence.txt
- Modified sequence (User Manual definition: Sequence representation including the post-translational modifications)
- Charge (User Manual definition: The charge-state of the precursor ion)
- Protein group IDs (User Manual definition: The identifier of the protein-group this redundant peptide sequence is associated with, which can be used to look up the extended protein information in the file ‘proteinGroups.txt’.)
proteinGroups.txt
- ProteinIDs (User Manual definition: Identifier(s) of protein(s) contained in the protein group)
- id (User Manual definition: A unique (consecutive) identifier for each row in the proteinGroups table, which is used to cross-link the information in this file with the information stored in the other files.)

DIA-NN

For flowTraceR the following columns are required:

Precursor.Id
Protein.Group (User Manual definition: inferred proteins)

Proteome Discoverer

For flowTraceR the following files and respective columns are required:

PSMs.txt
- Protein Accessions (User Manual definition: Displays the unique identifiers (accessions) of all proteins that include the given peptide sequence.)
- Annotated Sequence (User Manual definition: Displays the names of the flanking residues of a peptide in a protein.)
- Modifications (User Manual definition: Displays the static and dynamic modifications identified in the peptide.)
- Charge (User Manual definition: Displays the charge state of the peptide.)

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.