Documentation

Welcome

• Welcome to CoMPaseD
  • Purpose
  • Quick Start
  • Limitations
  • Citation

Setup

• Installation
  • Dependencies
    • Crux Toolkit
    • Python
    • Python packages

Documentation

• Graphical User Interface (GUI)
  • The Configuration tab
  • The Parameter tab
    • Fasta file
    • Output folder
    • Protease table
    • Protein binning
    • Deep MS-Peptide settings
    • Further settings
    • Protease score weights
    • Save/Load parameters
  • The Export tab
  • The Progress tab
  • The Results tab
• Command Line Interface (CLI)
  • Options
  • Advanced usage

References

• Configuration File
  • Default Configuration File
• Parameter File
  • List of Parameters
    • General Settings
    • Peptide Mapping & Protease Selection
    • Input & Output Files
    • Protease Digestion Parameters
    • Peptide Sampling & Coverage
    • Monte Carlo Simulation Parameters
    • Protein Abundance & Expression
    • Scoring Weights
    • Peptide Detectability Prediction by DeepMSPeptide
    • Additional Files
  • Default Parameter File
• Result Files
  • ProteinAbundance.tsv
  • RandomSampling.tsv
  • CoMPaseD_results.tsv
  • CoMPaseD_results_summary.tsv
• Frequently Asked Questions
• Citations