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A python interface to the SAGE search engine for mass spectrometry proteomics

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# sagepy
A python interface to the [SAGE](https://github.com/lazear/sage) search engine for mass spectrometry proteomics.

This repository hosts the main codebase for the sagepy project, which is dedicated to creating a fully functional Python interface for the powerful Sage search engine, originally written in Rust.

The project is structured as follows:

* `sagepy-connector`: This crate creates a Python interface using [PyO3](https://github.com/PyO3) to bind Rust to Python.
* `sagepy`: A pure Python, fully Pythonic wrapper around the exposed Rust code.
*	`qfdrust`: This crate implements basic false discovery rate (FDR) estimation using TDC, following the methods proposed by [Crema](https://github.com/Noble-Lab/crema).
*	`unimod`: A work-in-progress crate that bridges Sage-style PSM annotation with the UNIMOD standard.

Native mzML and MGF reading in `sagepy` is powered by the Rust crate [mzdata](https://github.com/mobiusklein/mzdata).

## Quickstart
Get started quickly by installing sagepy via pip:
```
pip install sagepy
```
Check out the tutorial notebooks to dive into [DB generation, searching, and FDR estimation](https://github.com/theGreatHerrLebert/sagepy/blob/main/sagepy/examples/scoring/scoring.ipynb), [peptide property prediction](https://github.com/theGreatHerrLebert/sagepy/blob/main/sagepy/examples/property-prediction/property_prediction.ipynb), and [re-scoring of results](https://github.com/theGreatHerrLebert/sagepy/blob/main/sagepy/examples/rescoring/rescoring.ipynb).

## Get involved
Do you have any questions or want to contribute? Feel free to reach out at any time!

## Acknowledgements
`sagepy` builds on a number of open-source Rust and Python projects. In particular, the native mzML and MGF reader path is implemented using [mzdata](https://github.com/mobiusklein/mzdata).

## Cite

If you find sagepy useful, please cite the original SAGE publication and consider citing our paper on sagepy:

Lazear, M. “Sage: An Open-Source Tool for Fast Proteomics Searching and Quantification at Scale.” [Journal of Proteome Research (2023)](https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00486).

Teschner, D et al. “Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.” [Journal of Proteome Research (2025)]( https://pubs.acs.org/doi/full/10.1021/acs.jproteome.4c00966).

Thanks for supporting free and open-source software and science!

sagepy

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