Mass spectrometry utility functions
Project description
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 3.8+ 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).
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
spectrum_utils-0.4.1.tar.gz
(1.0 MB
view hashes)
Built Distribution
Close
Hashes for spectrum_utils-0.4.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8121aa6bbd8feba7b830fff8d7af41278bd6a944d40b305d261099832b08dbea |
|
MD5 | 87d18e8e6c476b70c83bd429851476b1 |
|
BLAKE2b-256 | 13baeff9c8f494dfd69c36025070ec79a0d7ec68d5af352890df2fcdd7ab7137 |