User Guide

Some useful guides to help you get started with some functionalities of PyProphet.

• File Conversion
  • Feature File Conversion
  • Extracted Ion Chromatogram File Conversion
• Running a Full PyProphet Workflow (Parquet)
  • Feature File Conversion
  • Scoring OpenSWATH Results
• SCORE_ALIGNMENT Integration Workflow
  • Overview
  • High-Level Workflow
  • Detailed Component Workflow
  • Example Scenario
  • File Structure Examples
  • Key Benefits
  • Configuration Options
  • Output Columns