msbuddy
=======

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   :alt: Maintainer
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   :alt: PyPI
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   :alt: docs
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`msbuddy <https://github.com/Philipbear/msbuddy>`_ is developed for molecular formula annotation in mass spectrometry-based small molecule analysis.

**msbuddy** is able to provide formula annotations for:

  * queries with or without MS1 isotopic pattern
  * queries with or without MS/MS spectra
  * both positive and negative ionization modes

The minimum requirement for a **msbuddy** query is a single m/z value and its ionization polarity.

.. image:: https://github.com/Philipbear/msbuddy/blob/main/logo/logo.svg?raw=true
    :alt: Alternative text
    :align: center



**msbuddy** enables candidate space shrinkage via bottom-up MS/MS interrogation, accurate formula annotation via machine learning and false discovery rate estimation.
Please refer to `our paper <https://doi.org/10.1038/s41592-023-01850-x>`_ for more details.

Source codes are available at `GitHub <https://github.com/Philipbear/msbuddy>`_.

.. toctree::
   :caption: Contents
   :maxdepth: 1

   install
   quickstart
   config
   datain
   dataout
   pyapi
   cmdapi
   contact

Citation
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When using **msbuddy**, please cite:

  * S. Xing et al. `BUDDY: molecular formula discovery via bottom-up MS/MS interrogation <https://doi.org/10.1038/s41592-023-01850-x>`_. *Nature Methods* **20**, 881–890 (2023).

Contact
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Shipei Xing: philipxsp@hotmail.com

License
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**msbuddy** is licensed under the terms of the Apache License 2.0.