Oktoberfest: Rescoring, Collision Energy Calibration and Spectral Library Generation for Proteomics

Oktoberfest is a python tool for collision energy calibration, rescoring search results and generating spectral libraries for proteomics research within the Prosit ecosystem. It offers an end to end pipeline that takes search results, predicts peptide properties using koina, plots summaries and quality control figures and performs FDR estimation with either mokapot or percolator.

Key Contributors

• Mario Picciani: developer, maintainer

• Wassim Gabriel: developer, maintainer

• Matthew The: developer, maintainer

• Ludwig Lautenbacher: developer, maintainer

• Victor-George Giurcoiu: developer

• Omar Shouman: developer

• Firas Hamood: developer

• Cecilia Jensen: developer

• Julian Mueller: developer

• Mostafa Kalhor: developer

• Armin Soleymaniniya: developer

• Mathias Wilhelm: advisor and PI of wilhelmlab

Quickstart

• Discuss usage, development and issues on GitHub.

• Check our tutorial notebook, the usage principles or the API.

• Check the Contributor Guide if you want to participate in developing.

• Consider citing Oktoberfest along with original references.

News

Support for timsTOF added / spectral library generation overhaul 2024-01-31

Oktoberfest 0.6.0 is out supporting the new Prosit model for timsTOF data. Check out the preprint at BioRxiv.

Spectral library generation was completely overhauled, resulting in more stability, dramatic decreases in runtime and storage requirements and more customization in the config.

Note that this release introduces changes in the configuration file that might break your previous setup! Please check the new configuration format.

Oktoberfest now provides a low level API 2023-10-03

With our new release 0.5.0, we refactored our code base to provide a low level API to the users. Check the new API section for more details.

Please note: We dropped support for percolator version 3.05. Please update to version 3.06.1. See installation for details.

Oktoberfest is published! 2023-09-07

Alongside the new 0.4.0 release, Oktoberfest was published in Proteomics.

Check out the publication here: https://doi.org/10.1002/pmic.202300112.

Accordingly, please check How to cite.

The first Oktoberfest release is ready! 2023-06-25

Version 0.3.0 is available on PyPI.

We are happy to announce that our first standalone version of Oktoberfest is finally ready. Besides a lot of bugfixes, new features and performance enhancements over the existing online Prosit service at ProteomicsDB, the Oktoberfest codebase is now open source and available on GitHub. In addition, we switched to our new online prediction service koina which allows connecting Oktoberfest to any public or self-hosted koina instance for easy prediction model integration and being independent of ProteomicsDB!