Welcome

Join us for the joint scverse x single-cell proteomics hackathon on September 4-5, 2026 at the Vienna Biocenter in Vienna.

This hackathon aims to bring together users and developers of scverse tools with mass spectrometry-based single-cell proteomics (SCP) researchers. The main topic of this hackathon will center on the specialized preprocessing and downstream analysis workflows unique to SCP data.

During this hackathon, we will tackle core computational challenges, settle on robust data formats, and establish best practices for handling low-input MS signals. You will have the opportunity to directly improve existing tools, build missing pieces of the ecosystem, and optimize scverse packages for single-cell proteomics data. All contributions will be made publicly available on GitHub under an open-source license.

Hackathon Main Tasks

Task 1: Curation of Datasets

Task Lead: Florian Mutschler

Identifying, collecting, and preparing MS-based single-cell proteomics datasets to start a community-curated resource for testing analysis strategies and benchmarking methods such as imputation or normalization. Establishing AnnData format from the scverse ecosystem as the main object for benchmarking and analysis.

Task 2: Data QC and Preprocessing

Task lead: Jose Nimo

Identifying best practices for analyzing different types of MS-based single-cell proteomics datasets. Including: QC metrics, imputation strategies, normalization approaches, and methods for handling biological and technical confounders such as cell cycle, cell size, and batch effects. We aim to prototype methods in a service-styled package, to deal with these problems.

Task 3: Downstream analysis

Task lead: Anna Sophie Welter

Come together, think and benchmark different challenges during downstream analysis. How to perform feature selection? How can we use proteomics for cell type annotation?

Registration

Please fill out the following Luma form