spectrum_utils

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.

Installation

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

Documentation

Please see the documentation for detailed installation instructions, usage examples, the API reference, and more information.

Citation

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.