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.

.. image:: img/OpenSWATH_Workflow.svg

News
----

.. note::

   *2025-10-12:* Updated Docker image (openswath/openswath:0.3.0), and added an Apptainer image build for the latest development version of the OpenSWATH workflow, including OpenMS 3.4.1, PyProphet 3.0.2, easyPQP 0.1.53, sage 0.14.7, arycal 0.1.10, and DIAlignR 2.0.0

.. note::

   *2025-05-09:* With OpenMS 3.4.0, OpenSWATH supports automated spectrum addition at RT feature peak apex, peak picking extracted ion mobilograms, and ion mobility scoring for identifying transitions for IPF.

.. note::

   *2020-02-24:* With OpenMS 2.4.0, OpenSWATH supports ion mobility extraction and scoring (diaPASEF data), supports PRM data, supports metabolite assay library generation (via SIRIUS), extraction and scoring.

.. 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/singularity
   docs/binaries
   docs/sources

.. toctree::
   :maxdepth: 3
   :caption: Getting Started

   docs/getting_started

.. toctree::
   :maxdepth: 3
   :caption: Spectral library generation
   
   docs/generic
   docs/fragpipe
   docs/tpp
   docs/skyline
   docs/swathatlas
   docs/pqp

.. toctree::
   :maxdepth: 3
   :caption: Calibration libraries
   
   docs/calibration/generic
   docs/calibration/run_specific

.. 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
   docs/dialignr
   docs/arycal

.. toctree::
   :maxdepth: 3
   :caption: PTMs / Peptidoforms
   
   docs/ipf
   
.. toctree::
   :maxdepth: 3
   :caption: Chromatogram visualization
   
   docs/tapir
   docs/massdash

.. toctree::
   :maxdepth: 3
   :caption: Mobi-DIK (diaPASEF)
   
   docs/mobidik/mobi-dik
   docs/mobidik/dataconversion
   docs/mobidik/openswath_mobidik

.. toctree::
   :maxdepth: 3
   :caption: Differential expression analysis
   
   docs/swath2stats

.. toctree::
   :maxdepth: 3
   :caption: Tutorials
   
   docs/tutorials/diapasef_tutorial_1
   
Acknowledgments
---------------
The tools and workflows are being developed at the `Aebersold Group at IMSB, ETH Zurich <http://www.imsb.ethz.ch/research/aebersold.html>`_, `University of Toronto <http://roestlab.org/>`_ and `Columbia University <https://systemsbiology.columbia.edu/>`_ with contributions from others. The core components are implemented as part of the `OpenMS <http://www.openms.org>`_ framework, the `PyProphet <https://github.com/PyProphet>`_, and `msproteomicstools <https://github.com/msproteomicstools>`_ distributions.