msfiddle
========

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

.. rubric:: 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

.. rubric:: Contents

.. toctree::
   :maxdepth: 2

   usage
   formats
   api

.. rubric:: Reference

Hong et al. `FIDDLE: a deep learning method for chemical formula prediction from tandem mass spectra <https://www.nature.com/articles/s41467-025-66060-9>`_. *Nature Communications*, 2025.