Home

ProteoBench is an open platform for benchmarking proteomics data analysis workflows.

Get Started

ProteoBench in 5 steps

1. Choose a module to benchmark your proteomics data analysis workflow

2. Download the input data from the module page

3. Run your workflow on the input data

4. Upload the results to ProteoBench

5. Compare your workflow run with validated benchmark runs

ProteoBench Web App

Available ProteoBench modules

active

DDA quantification ion-level

Benchmark the ion-level quantification accuracy of label-free data dependent acquisition workflows using a multi-species sample

in development

DDA identification

Benchmark the identification sensitivity and specificity of data dependent acquisition workflows using an entrapment strategy

in development

DDA quantification peptidoform-level

Benchmark the peptidoform-level quantification accuracy of label-free data dependent acquisition workflows using a multi-species sample

in development

DIA quantification

Benchmark the quantification accuracy of label-free data independent acquisition workflows using a multi-species sample

proposed

De novo identification

Benchmark the identification sensitivity and specificity of de novo sequencing workflows

proposed

benchmark with Dynamic Organellar Mapping

Single-species benchmark using spacial proteomics

Module descriptions

Join the ProteoBench community

Submit your results as a validated benchmark run to be shared with the community.

Upload your results

Discuss modules, benchmarking runs, and comparisons with the community.

Discussion forum

Contribute to ProteoBench by developing new modules or improving existing ones.

GitHub repository

ProteoBench is

A project of

The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) is a community of bioinformaticians working in the field of mass spectrometry-based. EuBIC-MS aims to foster communication and collaboration between (computational) mass spectrometry researchers in Europe and beyond. Learn more at eubic-ms.org.

Funded by

Through EuBIC-MS, ProteoBench is continuously supported by the European Proteomics Association (EuPA). For specific events, such as the ProteoBench hackathon, ProteoBench has received funding from the Danish Data Science Academy (DDSA) and the Research Foundation - Flanders (FWO).

Supported by

Get in touch

Questions or comments? Email us at proteobench@eubic-ms.org.