The OpenSWATH Workflow enables targeted data analysis of data-independent acquisition (DIA) or SWATH-MS proteomic data. The main workflow consists of OpenSWATH, PyProphet, TRIC, IPF and TAPIR. This website provides documentation on installation and application of the tools.




2018-11-07: The Docker image now includes OpenMS 2.4.0 and PyProphet 2.0.1.


2018-11-07: With the release of OpenMS 2.4.0 and PyProphet 2.0.1, the new OpenSWATH workflow is available in the release branches.


2018-03-22: We provide an experimental Docker image for the latest development version of the OpenSWATH workflow.


2017-12-28: The tools of the OpenSWATH Workflow now provide experimental support for new SQLite-based file formats.

The OpenSWATH Workflow

Differential expression analysis


The tools and workflows are being developed at the Aebersold Group at IMSB, ETH Zurich, University of Toronto and Columbia University with contributions from others. The core components are implemented as part of the OpenMS framework, the PyProphet, and msproteomicstools distributions.