Home#
ProteoBench is an open platform for benchmarking proteomics data analysis workflows.
ProteoBench in 5 steps#
Choose a module to benchmark your proteomics data analysis workflow
Download the input data from the module page
Run your workflow on the input data
Upload the results to ProteoBench
Compare your workflow run with validated benchmark runs
Available ProteoBench modules#
active
Benchmark the ion-level quantification accuracy of label-free data dependent acquisition workflows using a multi-species sample
active
Benchmark the quantification accuracy of label-free data independent acquisition workflows (All-Ion Fragmentation - AIF) using a multi-species sample analysed with an Orbitrap
active
additional DIA ion-level module with DIA-PASEF data
active ^^^ additional DIA ion-level module with Astral DIA data
in development
Benchmark the identification sensitivity and specificity of data dependent acquisition workflows using an entrapment strategy
in development
Single-species benchmark using spacial proteomics
in development
Benchmark the peptidoform-level quantification accuracy of label-free data dependent acquisition workflows using a multi-species sample
in development
benchmarking identification and quantification workflows for low-input and single cell proteomics (SCP)
proposed
Benchmark the identification sensitivity and specificity of de novo sequencing workflows
proposed
Benchmark phosphopeptide identification workflows and assess their identification and localization accuracy
proposed
Benchmarking with a high dynamic range multispecies dataset
Join the ProteoBench community#
Submit your results as a validated benchmark run to be shared with the community.
Discuss modules, benchmarking runs, and comparisons with the community.
Contribute to ProteoBench by developing new modules or improving existing ones.
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), the Research Foundation - Flanders (FWO), and Core For Life.
Supported by#
Get in touch#
Questions or comments? Email us at proteobench@eubic-ms.org.