Introduction

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

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])

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.)

For flowTraceR the following columns are required:

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.)