# spectrum_utils

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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)](https://www.psidev.info/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](https://www.psidev.info/proforma) 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.
 
## Citation
 
spectrum_utils is freely available as open source under the [Apache 2.0 license](http://opensource.org/licenses/Apache-2.0).

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](https://doi.org/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](https://doi.org/10.1021/acs.jproteome.2c00632).

```{toctree}
---
caption: Contents
maxdepth: 1
---

install
quickstart
annotating
plotting
runtime
api
contact
```