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Introduction

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.

News

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.

The OpenSWATH Workflow

.. 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

Acknowledgments

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.

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