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bittremieux-lab/spectrum_utils: Python package for efficient mass spectrometry data processing and visualization
spectrum_utils is a Python package for efficient mass spectrometry data processing and visualization.
spectrum_utils contains the following features:
- Spectrum loading from online proteomics and metabolomics data resources using the Universal Spectrum Identifier (USI) mechanism.
- Common spectrum processing operations (precursor & noise peak removal, intensity filtering, intensity scaling) optimized for computational efficiency.
- Annotating observed spectrum fragments using the ProForma 2.0 specification for (modified) peptidoforms.
- Publication-quality, fully customizable spectrum plotting and interactive spectrum plotting.
spectrum_utils requires Python version 3.10+ and can be installed with pip or conda.
Using pip:
pip install spectrum_utils[iplot]
Using conda:
conda install -c bioconda spectrum_utils
Please see the documentation for detailed installation instructions, usage examples, the API reference, and more information.
spectrum_utils is freely available as open source under the Apache 2.0 license.
When using spectrum_utils, please cite the following manuscripts:
- Wout Bittremieux. "spectrum_utils: A Python package for mass spectrometry data processing and visualization." Analytical Chemistry 92, 659--661 (2020) doi:10.1021/acs.analchem.9b04884.
- Wout Bittremieux, Lev Levitsky, Matteo Pilz, Timo Sachsenberg, Florian Huber, Mingxun Wang, Pieter C. Dorrestein. "Unified and standardized mass spectrometry data processing in Python using spectrum_utils" Journal of Proteome Research 22, 625--631 (2023) doi:10.1021/acs.jproteome.2c00632.
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