A python interface to the 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 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.unimod: A work-in-progress crate that bridges Sage-style PSM annotation with the UNIMOD standard.
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, peptide property prediction, and re-scoring of results.
Do you have any questions or want to contribute? Feel free to reach out at any time!
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).
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).
Thanks for supporting free and open-source software and science!