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 ion-level label-free quantification accuracy of DDA workflows using a multi-species (HYE) sample on an Orbitrap Astral instrument.
active
Benchmark ion-level label-free quantification accuracy of DDA workflows using a multi-species (HYE) sample on an Orbitrap QExactive instrument.
active
Benchmark peptidoform-level label-free quantification accuracy of DDA workflows using a multi-species (HYE) sample on an Orbitrap QExactive instrument.
active
Benchmark ion-level label-free quantification accuracy of DIA workflows using a multi-species (HYE) sample on an Orbitrap Astral instrument.
active
Benchmark ion-level label-free quantification accuracy of DIA-PASEF workflows using a multi-species (HYE) sample on a timsTOF instrument.
active
Benchmark ion-level label-free quantification accuracy of DIA (Zeno SWATH) workflows using a multi-species (HYE) sample on a ZenoTOF 8600 instrument.
in development
Benchmark the identification sensitivity and specificity of de novo sequencing workflows using DDA-HCD data.
in development
Benchmark ion-level label-free quantification accuracy of DIA workflows using a high dynamic range human plasma multi-species (PYE) sample.
in development
Benchmark identification and quantification workflows for low-input and single-cell proteomics using DIA acquisitions.
archived
Benchmark ion-level label-free quantification accuracy of DIA (All-Ion Fragmentation) workflows using a multi-species (HYE) sample on an Orbitrap instrument.
Modules in discussion#
benchmark with Dynamic Organellar Mapping — Single-species benchmark using spatial proteomics.
DDA identification - phosphopeptides — Benchmark phosphopeptide identification workflows and assess their identification and localization accuracy.
Identification with DDA — Benchmark the identification sensitivity and specificity of data dependent acquisition workflows using an entrapment strategy.
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.