ChromaKit-MS is a Python application for inspecting and processing GC-MS (Gas Chromatography–Mass Spectrometry) data. The project provides a PySide6 based graphical interface that allows users to load Agilent .D directories, apply chromatogram processing steps and perform MS library searches.
- Chromatogram processing – smoothing, baseline correction and peak detection via
pybaselinesandscipyutilities. - Peak integration – integrate detected peaks and export results.
- Mass spectrum search – optional search against spectral libraries using
ms-toolkit-nrel. - Batch automation – process a list of data directories without manual interaction.
- Interactive plots – inspect chromatograms, TIC traces and extracted mass spectra with Matplotlib.
- Python 3.7+
- PySide6
- rainbow-api (for reading Agilent data)
- NumPy, SciPy, Matplotlib and pybaselines
Optional features such as MS library searching require ms-toolkit-nrel.
Clone the repository and install in editable mode:
pip install -e .This installs the chromakit-ms console entry point which launches the GUI.
chromakit-msUse the file tree on the left of the window to select an Agilent .D directory. The application will display the chromatogram and TIC, allowing you to adjust processing parameters, integrate peaks and export results. Refer to the on-screen controls and dialogs for automation and MS search options.
logic/ Data loading, processing and integration
ui/ PySide6 interface implementation
resources/ Icons and other static resources
main.py Application entry point
setup.py Package metadata and entry point
ChromaKit-MS is released under the terms of the Apache License 2.0. The distribution also includes or links to third-party components under their own licenses:
ms-toolkit-nrel– Apache License 2.0rainbow-api– GNU Lesser General Public License v3.0pybaselines– BSD 3-Clause License
See the NOTICE file for attribution and additional details.