hxex tutorial: HSPB5 and two disease-associated variants
=========================================================

This folder holds the data for the hxex tutorial. The tutorial itself is in two parts:

    https://github.com/tuttlelm/hxex/blob/main/docs/guide/tutorial.md        (part 1)
    https://github.com/tuttlelm/hxex/blob/main/docs/guide/tutorial-fits.md   (part 2)

The same steps are in the two Jupyter notebooks in this folder, for those who prefer to work
in a notebook: hxex_b5_tutorial_1_basics.ipynb, then hxex_b5_tutorial_2_fits.ipynb.


What is in this folder
----------------------

SpecExport/              HDX-MS spectra exported from HDExaminer 3.0 ("SpecExport"):
  WT/, D109H/, R120G/    one folder per sample, one folder per peptide inside it, one
                         file per time point, replicate, and charge state
  WT.fasta, ...          the protein sequence of each sample
hxex_b5_tutorial_1_basics.ipynb   part 1 of the tutorial as a Jupyter notebook
hxex_b5_tutorial_2_fits.ipynb     part 2, which continues from the results of part 1
tutorial_helpers.py      small helpers the notebooks use to add rules to the project file
                         and fill in the review table
README.txt               this file
LICENSE.txt              the licence of the data (CC BY 4.0)


The data
--------

The spectra are from the hydrogen/deuterium exchange experiments of:

    Woods CN, Janowska MK, Ulmer LD, Kaur Sidhu J, Stone NL, James EI, Guttman M, Bush MF,
    Klevit RE. Activation mechanism of small heat shock protein HSPB5 revealed by
    disease-associated mutants. Proc Natl Acad Sci USA 122(20), e2425061122 (2025).
    https://doi.org/10.1073/pnas.2425061122

Please cite this paper when you use the data.

In short: HSPB5 (wild type, D109H and R120G; 0.04 mg/mL) labelled at room temperature in
85 % D2O PBS, pH 7.5, for 4 s, 1 min, 30 min, and 20 h; fully deuterated controls made in
85 % D2O at 75 degrees C for 30 min; quenched with ice-cold 1.6 % formic acid; measured on a
Waters Synapt G2-Si. The folders also hold 0.1 s and 0.8 s time points (quench-flow) that
are not part of the paper; the tutorial shows how to leave them out.


Licence
-------

The data in this folder are licensed under the Creative Commons Attribution 4.0
International licence (CC BY 4.0): https://creativecommons.org/licenses/by/4.0/
You may share and adapt them for any purpose, provided you give appropriate credit (cite
the paper above).
