fluoride_contamination

This repository contains data and input files for the manuscript 'Micromolar fluoride contamination arising from glass NMR tubes and a simple solution for biomolecular applications' by Matwani et al.

These data and Jupyter notebooks support the manuscript entitled "Micromolar fluoride contamination arising from glass NMR tubes and its simple removal" by Matwani, Cornish, DeBenedictis and Heller.

Requirements: python 3.x, install jupyter notebook, matplotlib, numpy, scipy.

Install nmrglue following https://nmrglue.readthedocs.io/en/latest/install.html (in command line: $ python -m pip install nmrglue)

This dataset contains: 19F Nuclear Magnetic Resonance (NMR) spectroscopy data files (.ft2 format) including:

1. 1D spectra of Sodium Fluoride (NaF) standards, from 1uM to 100 uM, in Standards_19F_1D_spectra/
2. 1D spectra of PBS buffer incubated in NMR glass tubes over 48 hours, in Brands_19F_1D_spectra/
3. 1D spectra of PBS incubated in an NMR quartz tube, and pre- and post-rinsing a glass tube with PBS, in Nulls_19F_1D_spectra/
4. 1D spectra of fluorinated compounds and the fluoride peak, in Compounds_19F_1D_spectra/
5. 1D spectra of PBS incubated in an NMR glass tube over time, in Timecourse_19F_1D_spectra/ (processed using a separate Jupyter notebook)
6. 1D spectra of 20 uM NaF in the presence and absence of various proteins, in D2D3_19F_1D_spectra/, DNase_19F_1D_spectra/ and BSA_19F_1D_spectra/
7. 1D spectra of different buffers incubated in NMR glass tubes over 48 hours, in pH_19F_1D_spectra/

The Jupyter notebook "19F_1D_spectra_plot.ipynb" processes the directories in the same order as above, and generates .svg files in the Results/ directory.

The outputs are:

• Spectra of the sodium fluoride standards coloured different shades of blue based on [NaF].
• Standard curve of the integral of the NaF standards with calculated fluoride integrals of buffer in glass tubes annotated in purple.
• Spectra of buffer in glass tubes annotated with symbols corresponding to the standard curve.
• Spectra of buffer in quartz tube after incubation, and buffer in glass tube pre- and post-rinse.
• Spectra of fluorinated compounds with known/unknown concentrations of fluoride.
• Spectra of the fluoride peak in the presence and absence of NS5a D2D3, BSA and DNase.
• Spectra of the fluoride peak after incubated glass tubes with different buffers over 48 hours.

Blue is assigned to data collected using quartz tubes, and purple is assigned to data collected using glass tubes.

The Jupyter notebook "19F_1D_timecourse.ipynb" processes the Timecourse_19F_1D_spectra/ directory, and generates an .svg file in the Results/ directory. The output is:

• A fitted curve generated by calculating the integral of the peak over time, normalised using the average integral value of 100 uM NaF.

Credits:

This project includes code snippets from the following sources:

• The 1D spectra processing workflow in Jupyter notebooks "19F_1D_spectra_plot.ipynb" and "19F_1D_timecourse.ipynb" is adapted from the work of Gabriella Heller (https://github.com/gthh2/ns5a-d2d3_small_mol/blob/master/19F_1D/plot_19F_1D_data.ipynb).
• The fit_raw.py file used to fit the spectra was provided by Gabriella Heller (https://github.com/gthh2/ns5a-d2d3_small_mol/blob/master/19F_1D/)