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spectrum_utils

conda PyPI Build status docs

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 3.8+ 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" bioRxiv (2022).

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Python package for efficient mass spectrometry data processing and visualization

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