KinetX is a scientific software dedicated to the processing of (bio)chemical kinetics experiments by NMR. KinetX extracts 1D spectra acquired as pseudo 2D spectra, performs Fourier-transform, phasing and beseline correction on each 1D spectra, and extract chemical shifts, intensity and area of the signal(s) of interest.
It is one of the routine tools that we use at the MetaSys team and MetaToul platform for quantitative analysis of enzymatic or chemical kinetics experiments.
The code is open-source, and available under a GPLv3 license.
KinetX requires TopSpin 3.0 or higher (tested on 3.0PL3 to 3.5PL7) and run on all plate-forms.
To install KinetX:
Unpack the content of KinetX.zip somewhere on your disk, and copy the file 'kinetx.py' in the python program folder of your TopSpin user directory (by default: /exp/stan/smr/py/usr)
To use KinetX:
KinetX requires as input a pseudo 2D spectra which must be Fourier-transformed in F2.
-
Open the pseudo 2D spectra to process.
-
Define the window that contains the signal of interest in the 2D spectra (only the most intense peak of the displayed area wil be processed)
-
Run KinetX by typing 'kinetx' in the TopSpin command, enter the signal name (used for spectra annotation), the total number of experiments to process, and confirm the information provided
-
Processing results will be displayed and saved in the res subdirectory of the TopSpin experiments folder
Results
The folder res is created in the data subdirectory containing all the experiments, and results are stored in the file 'results.txt':
-
PeakName: name of the signal
-
PeakID: ID of the peak in TopSpin
-
Slice: slice of the spectrum (increment in F2)
-
F1: F1 chemical shift (ppm)
-
dwF1: difference of chemical shifts in F1 compared to the reference spectrum, which is the first expno (ppm)
-
Intensity: peak intensity
-
resF1: FWHM in F1 dimension (ppm)
Error messages are explicit. After correcting the problem, rerun KinetX.
If you have an idea on how we could improve KinetX please submit a new issue to our GitHub issue tracker.
Contributions are very welcome! ❤️
Please work on your own fork.
Cox, N., et al. An integrated pH meter during reaction monitoring with dual reception 1H, 31P NMR spectroscopy (submitted)
Pierre Millard, Neil Cox, Guy Lippens
📧 Pierre Millard, millard@insa-toulouse.fr