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 peptidoform-level quantification accuracy of label-free data dependent acquisition workflows using a multi-species sample. Data associated to this module is the same as for the module Quant LFQ DDA precursors (QExactive).
active
Benchmark the ion-level quantification accuracy of label-free data dependent acquisition workflows using a multi-species sample
active
additional DIA ion-level module with DIA-PASEF data
active
additional DIA ion-level module with Astral DIA data
in development
Single-species benchmark using spatial proteomics
in development
benchmarking identification and quantification workflows for low-input and single cell proteomics (SCP)
in development
Benchmark the identification sensitivity and specificity of de novo sequencing workflows
in discussion
Benchmark phosphopeptide identification workflows and assess their identification and localization accuracy
in discussion
Benchmarking with a high dynamic range multispecies dataset
in discussion
Benchmark the identification sensitivity and specificity of data dependent acquisition workflows using an entrapment strategy
archived
Benchmark the quantification accuracy of label-free data independent acquisition workflows (All-Ion Fragmentation - AIF) using a multi-species sample analysed with an Orbitrap. A discussion on oxidation-related issues with the data used for this module can be found here: orgs/Proteobench#641.
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.