PIGEON-FEATHER (Peptide ID Generation for Exchange Of Nuclei-Free Energy Assignment Through Hydrogen Exchange Rates): a method for calculating free energies of opening (∆Gop) at single- or near-single-amino acid resolution for protein ensembles of all sizes from hydrogen exchange/mass spectrometry (HX/MS) data.
PIGEON-FEATHER can be used from Jupyter Notebook (recommended), or by writing Python scripts. The documentation can be found at http://glasgowlab.org/PIGEON-FEATHER.
The tutorials notebooks could be found at docs/source/tutorials.
HXMS is a unified, lightweight, and human-readable file format that preserves full isotopic envelopes and experimental conditions for HX/MS data. We recommend using HXMS with FEATHER. HXMS files can be generated using PFLink, which supports exports from BioPharma Finder, HDExaminer, DynamX, and HDX Workbench.
You can easily read and write HXMS files using FEATHER:
from pigeon_feather.hxio import load_HXMS_files, write_HXMS_files
hdxms_data = load_HXMS_files(["./ecDHFR_APO.hxms",
"./ecDHFR_TRI.hxms"])
write_HXMS_files([hdxms_data], protein_name="ecDHFR", output_dir=".")# install mamba
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh
# create a conda environment and install the required packages
conda create --name pigeon_feather python=3.11
conda activate pigeon_feather
conda install jupyterlab mdanalysis numba
conda install pymol-open-source
pip install pyopenms hdxrate
# clone the PIGEON-FEATHER repo
git clone https://github.com/glasgowlab/PIGEON-FEATHER.git
# clone the bayesian hdx iso repo
git clone https://github.com/lucl13/bayesian_hdx.git
cd PIGEON-FEATHER
pip install .
cd ../bayesian_hdx
pip install .
docker build -f docker/Dockerfile -t pigeon_feather:0.9 .
docker run -it -v $(pwd):/work -p 8889:8889 --rm pigeon_feather:0.9 jupyter-lab --port 8889
click the link in the terminal to open the jupyter notebook cd to example/docker_example click and run
NOTE: bayesian_hdx at the above link is a fork of the original repo at https://github.com/salilab/bayesian_hdx with some modifications to the code to make it compatible with the PIGEON-FEATHER and support for the isotopic envelope fitting.
If you use PIGEON-FEATHER in scientific work, please cite:
Lu, C.; Wells, M. L.; Reckers, A.; McBride, S. K.; Glasgow, A. Site-Resolved Energetic Information from HX–MS Experiments. Nat Chem Biol 2025, 1–11. (*equal contributions) https://doi.org/10.1038/s41589-025-02049-1