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.
Note
2018-11-07: The Docker image now includes OpenMS 2.4.0 and PyProphet 2.0.1.
Note
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.
Note
2018-03-22: We provide an experimental Docker image for the latest development version of the OpenSWATH workflow.
Note
2017-12-28: The tools of the OpenSWATH Workflow now provide experimental support for new SQLite-based file formats.
.. toctree:: :maxdepth: 3 :caption: Installation docs/docker docs/binaries docs/sources
.. toctree:: :maxdepth: 3 :caption: Getting Started docs/getting_started
.. toctree:: :maxdepth: 3 :caption: Spectral library generation docs/generic docs/tpp docs/skyline docs/swathatlas docs/pqp
.. toctree:: :maxdepth: 3 :caption: Targeted data extraction docs/openswath
.. toctree:: :maxdepth: 3 :caption: Statistical validation docs/pyprophet docs/percolator
.. toctree:: :maxdepth: 3 :caption: Multi-run alignment docs/tric
.. toctree:: :maxdepth: 3 :caption: PTMs / Peptidoforms docs/ipf
.. toctree:: :maxdepth: 3 :caption: Chromatogram visualization docs/tapir
.. toctree:: :maxdepth: 3 :caption: Mobi-DIK docs/mobi-dik docs/dataconversion docs/installation docs/librarygeneration docs/openswath_mobidik
.. toctree:: :maxdepth: 3 :caption: Differential expression analysis docs/swath2stats
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.