msfiddle

msfiddle is a Python package for predicting chemical formulas from tandem mass spectra (MS/MS) using deep learning.

Features

• Formula prediction from MS/MS spectra via pre-trained TCN models

• Formula refinement with FDR-based confidence scoring

• Support for Orbitrap and Q-TOF instruments

• Optional integration with BUDDY and SIRIUS

Contents

• Usage
  • Installation
  • Downloading Pre-trained Models
  • Running Predictions
  • Integration with BUDDY and SIRIUS
  • Python API
• File Formats
  • Input: MGF
  • Output: msfiddle CSV
  • Input: BUDDY CSV (optional)
  • Input: SIRIUS CSV (optional)
• API Reference
  • Prediction API
  • Molecular Utilities
  • MS/MS Utilities
  • Formula Refinement

Reference

Hong et al. FIDDLE: a deep learning method for chemical formula prediction from tandem mass spectra. Nature Communications, 2025.