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About 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.

See the documentation for more information and detailed examples on how to get started with spectrum_utils for versatile mass spectrometry data manipulation in Python.


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.