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Feature/mobi dik #19

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6ef7831
minor fix
klannieha Jun 12, 2019
f495641
example
klannieha Jun 13, 2019
f534f1a
added example to osw pqp
klannieha Aug 13, 2019
e107386
added link to irt from Hela
May 22, 2020
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26 changes: 23 additions & 3 deletions docs/librarygeneration.rst
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Expand Up @@ -66,17 +66,37 @@ Alternatively, we also have a script as a commandline tool that can be called wi

.. code:: bash

python create_library.py
create_library.py

For details and options of the script, simply type:

.. code:: bash

python create_library.py --help
create_library.py --help

Here is an example for running the commandline tool:

.. code:: bash

create_library.py --pasefdata pasef_analysis_path.d/\
--mqout MaxQuant_output_dir \
--irt iRT_file.tsv \
--outfile mqout.tsv \
--rt_alignment nonlinear \
--im_alignment linear



Generating Assay Library
^^^^^^^^^^^^^^^^^^^^^^^^

After generating the spectral library with diapysef, the ``tsv`` file can be imported into ``OpenSwathAssayGenerator`` and ``OpenSwathDecoyGenerator`` as documented in :doc:`pqp`
After generating the spectral library with diapysef, the ``tsv`` file can be imported into ``OpenSwathAssayGenerator`` and ``OpenSwathDecoyGenerator`` as documented in :doc:`pqp`.

Here is an example for running the tools taking the files generated from ``create_library.py`` above:

.. code:: bash

OpenSwathAssayGenerator -in mqout.tsv -out assay_lib.pqp -swath_windows_file setup.tsv

OpenSwathDecoyGenerator -in assay_lib.pqp -out assay_lib_target_decoy.pqp -method pseudo-reverse -switchKR true

3 changes: 3 additions & 0 deletions docs/mobi-dik.rst
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Expand Up @@ -71,6 +71,9 @@ Output of the scheme can also be plotted over the MaxQuant outputs in the mz and
Data
----

The iRT library file generated for HeLa cell lysate using common peptides across triplicate HeLa DDA can be obtained here `iRT files <https://drive.google.com/drive/folders/19QvyNQCCanBZ_JZ6YaLQq-45GmmX9RyI?usp=sharing>`_.


TODO

References
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9 changes: 6 additions & 3 deletions index.rst
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@@ -1,6 +1,9 @@
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.
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

Expand All @@ -13,7 +16,8 @@ News

.. 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.
*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::

Expand Down Expand Up @@ -88,7 +92,6 @@ The OpenSWATH Workflow

docs/mobi-dik
docs/dataconversion
docs/installation
docs/librarygeneration
docs/openswath_mobidik

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