Overview of ProteoBench#
ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows.
ProteoBench provides a centralized web platform for developers and end-users to compare proteomics data analysis pipelines. This community-curated effort will allow for an easy and controlled comparison of tools developed or used by the participants to other state-of-the-art pipelines for specific applications. The goal is not to select a single best one-fits-all data analysis workflow, but to allow:
end-users to identify a good workflow to fulfill their specific needs
developers to identify the specific strengths and weaknesses in their workflows, guiding the development process
the field to easily position a newly published workflow within the context of the existing state-of-the-art
Description#
Participants (both end-users and developers) can download a set of input files (e.g., raw MS files, search databases, or spectral libraries) tailored to specific benchmark metrics. They can then analyze the data with any workflow, and upload the results in a homogenized format. A set of metrics will be retrieved or calculated from these results and can be visualized alongside all the other metrics calculated from the results of other participants (or of curated benchmark runs).
Goals and non-goals#
ProteoBench:
Allows for an easy and controlled comparison of existing data analysis workflows
Provides a frame of reference for newly developed workflows
Documents and implements benchmarks that each highlight strengths or weaknesses of data analysis workflow (steps)
Evolves continuously, according to the needs of the field
DOES NOT point to a single best one-fits-all data analysis workflow
SHOULD NOT be used as evidence for generalized statements about a workflow’s performance
SHOULD NOT be used by developers as single performance measure of their workflow
Organization#
The github repository for ProteoBench can be found here.
ProteoBench documentation is divided into two main parts:
The different ProteoBench benchmark modules that exist, how they evolve and how to used them.
The Developer guide provides information on the structure of the project and how to contribute.
Contact us#
email us here.
Contribution#
People who contributed to ProteoBench (in alphabetical order)