From 6ef78318905f5b02bc0a4b0e8678fc6d2214935d Mon Sep 17 00:00:00 2001 From: unknown Date: Wed, 12 Jun 2019 16:24:50 -0400 Subject: [PATCH 1/4] minor fix --- docs/librarygeneration.rst | 6 +++--- index.rst | 9 ++++++--- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/docs/librarygeneration.rst b/docs/librarygeneration.rst index 3a2173a..9ae302d 100644 --- a/docs/librarygeneration.rst +++ b/docs/librarygeneration.rst @@ -66,17 +66,17 @@ 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 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`. diff --git a/index.rst b/index.rst index e9980bc..ae3b917 100644 --- a/index.rst +++ b/index.rst @@ -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 @@ -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:: @@ -88,7 +92,6 @@ The OpenSWATH Workflow docs/mobi-dik docs/dataconversion - docs/installation docs/librarygeneration docs/openswath_mobidik From f4956419e6399ca3621169546766dd9d1882953e Mon Sep 17 00:00:00 2001 From: unknown Date: Thu, 13 Jun 2019 14:23:43 -0400 Subject: [PATCH 2/4] example --- docs/librarygeneration.rst | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/docs/librarygeneration.rst b/docs/librarygeneration.rst index 9ae302d..f481650 100644 --- a/docs/librarygeneration.rst +++ b/docs/librarygeneration.rst @@ -74,6 +74,18 @@ For details and options of the script, simply type: 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 ^^^^^^^^^^^^^^^^^^^^^^^^ From f534f1aee184226febe3e8229186e9b843e23495 Mon Sep 17 00:00:00 2001 From: unknown Date: Tue, 13 Aug 2019 17:43:28 -0400 Subject: [PATCH 3/4] added example to osw pqp --- docs/librarygeneration.rst | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/librarygeneration.rst b/docs/librarygeneration.rst index f481650..7a9c800 100644 --- a/docs/librarygeneration.rst +++ b/docs/librarygeneration.rst @@ -92,3 +92,11 @@ 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`. +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 + From e10738695dbb9e65ed38f15cc6012e2e723df33a Mon Sep 17 00:00:00 2001 From: Annie Ha Date: Fri, 22 May 2020 14:49:49 -0400 Subject: [PATCH 4/4] added link to irt from Hela --- docs/mobi-dik.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/mobi-dik.rst b/docs/mobi-dik.rst index 2d61d52..3aaa7a1 100644 --- a/docs/mobi-dik.rst +++ b/docs/mobi-dik.rst @@ -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 `_. + + TODO References