sagepy

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.

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, peptide property prediction, and re-scoring of results.

Get involved

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