Author: Oliver Kardell

# 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.)