Requirements

In flowTraceR: Tracing Information Flow for Inter-Software Comparisons in Mass Spectrometry-Based Bottom-Up Proteomics

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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.)

flowTraceR documentation built on June 8, 2025, 1:23 p.m.