OpenMS · tapaswenipathak · Jun 10, 2022 · Jun 7, 2022 · Jun 8, 2022 · Jun 8, 2022
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -31,14 +31,15 @@ For any questions, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/Op
 6. Use `backtick`(s) for formatting code, library name, files, and path.
 7. Use **bold** for product name, object name, an independent entity.
 8. Use **bold** for menu title in an application.
-9. Link to glossary terms using {term}`this is a glossary term`.
+9. Link to glossary terms using {term}\`this is a glossary term\`.
 10. OpenMS documentation uses following Admonitions
     - Hint
 	- Important
 	- Note
 	- Warning
 	- Tip
 	- See Also
+
 	Example of these are present in documentation, please follow them.
 11. Always specify lexers for code blocks.
 12. Format keyboard strokes using `<kbd>qwerty-keyboard-button</kbd>`, as an example, please see [this](../docs/tutorials/TOPP/hotkeys-table.md) file.

diff --git a/conf.py b/conf.py
@@ -36,6 +36,16 @@
   'sphinx_inline_tabs',
 ]
 
+myst_enable_extensions = [
+  "tasklist",
+  "dollarmath",
+  "amsmath",
+  "colon_fence",
+  "linkify",
+  "replacements",
+  "linkify_fuzzy_links",
+]
+
 autosummary_generate = True
 autosummary_imported_members = True
 

diff --git a/docs/contact-us.md b/docs/contact-us.md
@@ -1,7 +1,7 @@
 Contact Us
 =========
 
-Join us on [Discord](https://discord.com/invite/swkxs72CHB)!
+Join us on [Discord](https://discord.gg/WxynEEsf5X)!
 
 You can also contact us:
 

diff --git a/docs/glossary.md b/docs/glossary.md
@@ -102,9 +102,6 @@ Collision-induced dissociation (CID)
 TOPP
   The OpenMS Proteomics Pipeline.
 
-TOPPAS.app
-  TOPPAS allows to create, edit, open, save, and run TOPP workflows.
-
 MSGFPlusAdapter
   Adapter for the MS-GF+ protein identification (database search) engine. More information is available [here](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MSGFPlusAdapter.html).
 

diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md
@@ -19,14 +19,25 @@ Before using OpenMS, become familiar with the following terms:
 |--------------------|-------------|
 |**TOPPView**        |A tool that is used to view and explore {term}`LC-MS` data, alignments, groups, peptide identifications, and more.|
 |**TOPPAS**          |A graphical workflow design tool that is used to create pipelines from all {term}`TOPP tools` (and {term}`UTILS`).|
-|**TOPP tools**      |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)|
-|**UTILS**           |Similar to {term}`TOPP tools`, but with more supporting character, which are rarely used in a productive pipeline, but rather during pipeline construction or parameter optimization. See also: [UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)|
+|**TOPP tools**      |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp-and-utils/topp-and-utils.md)|
+|**UTILS**           |Besides {term}`TOPP`, OpenMS offers range of other tools. They are not included in {term}`TOPP` as they are not part of typical analysis pipelines. A set of command line utilities, similar to {term}`TOPP tools`, mostly used during pipeline construction or parameter optimization. |
+
+```{seealso}
+
+[UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)|
+```
+
+```{important}
+Users can now use {term}`KNIME` in place of {term}`TOPPAS`; the later will deprecated with no support in near future.
+Please find more information about using {term}`KNIME` in [KNIME tutorial](../../tutorials/KNIME/KNIME-tutorial.md).
+```
+
 
 ## How to run a Tool
 
 A good start are the example pipelines (select **File** > **Open example file** within {term}`TOPPAS`).
 
-Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp/topp.md) and the one of ([TOPPAS tutorial](../../tutorials/TOPPAS/TOPPAS-tutorial.md)).
+Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp-and-utils/topp-and-utils.md) and the one of ([TOPPAS tutorial](../../tutorials/TOPPAS/TOPPAS-tutorial.md)).
 
 Alternatively, use the command line and call tools directly. In this case, you'll probably want to use some type of shell
 script for automation.
@@ -48,7 +59,7 @@ The default parameters of each tool can usually be tweaked to fit the data and i
 
    e.g. `FileFilter -write_ini filefilter.ini`
 
-   Now, edit the INI file (which is a XML file) using the [INIFileEditor](../../topp/ini-file-editor.md), which is another GUI tool shipped with
+   Now, edit the INI file (which is a XML file) using the [INIFileEditor](../../topp-and-utils/ini-file-editor.md), which is another GUI tool shipped with
    OpenMS and similar to the one build into {term}`TOPPAS`.
 
 ### How do I feed the INI file to a Tool?

diff --git a/docs/images/tutorials/topp/TOPPView_help.png b/docs/images/tutorials/topp/TOPPView_help.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -71,8 +71,8 @@ Contents
    :maxdepth: 2
    :caption: OpenMS TOPP Tools
 
-   topp/topp.md
-   topp/adding-new-tool-to-topp.md
+   topp-and-utils/topp-and-utils.md
+   topp-and-utils/adding-new-tool-to-topp.md
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md
@@ -5,16 +5,6 @@ Installation on GNU/Linux
 
 Use conda or bioconda to install OpenMS.
 
-1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html).
-2. Install OpenMS using conda:
-   `conda install -c openms openms`
-3. Other OpenMS packages can be installed using:
-   ```
-   conda install -c openms pyopenms
-   conda install -c openms openms-thirdparty
-   conda install -c openms libopenms
-   ```
-
 ```{tab} openms
 openms contains OpenMS C++ Tools.
 ```
@@ -32,6 +22,16 @@ openms-thirdparty are external tools that are wrapped in OpenMS with adapters. T
 the openms package.
 ```
 
+1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html).
+2. Install OpenMS using conda:
+   `conda install -c openms openms`
+3. Other OpenMS packages can be installed using:
+   ```
+   conda install -c openms pyopenms
+   conda install -c openms openms-thirdparty
+   conda install -c openms libopenms
+   ```
+
 To install using bioconda:
 
 ```
@@ -85,13 +85,8 @@ These packages are not directly maintained by the OpenMS team and they can not b
 same behaviour as when building it from source code. Also, their availability and version is subject to change and
 support might be limited (due to unforeseen or untested behaviour). It is suggested not to install them parallel to our
 Debian package.
-
 ```
 
-## Installation via building from source code
-
-The source code of OpenMS is available on GitHub. Follow [Building OpenMS on GNU/Linux](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/install_linux.html) instructions on how to build OpenMS from source.
-
 ```{note}
 Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.
 ```
@@ -102,8 +97,17 @@ Make sure you have [Docker installed](https://docs.docker.com/engine/install/).
 
 Our Docker support is constantly updated. Images can be obtained via [ghcr.io](https://ghcr.io).
 
-1. [openms-executables](https://ghcr.io/openms/openms-executables:latest)
-2. [openms-library](https://ghcr.io/openms/openms-library:latest)
+```{tab}
+
+[openms-executables](https://ghcr.io/openms/openms-executables:latest)
+
+```
+
+```{tab}
+
+[openms-library](https://ghcr.io/openms/openms-library:latest)
+
+```
 
 Or via [BioContainers Registeries](https://biocontainers.pro/registry).
 
@@ -116,9 +120,9 @@ Docker images can be pulled via or one of the following commands:
 
 ```
 docker pull biocontainers/openms
-docker pull openms/library
-docker pull openms/executables
-docker pull openms/pyopenms
+docker pull biocontainers/libopenms
+docker pull biocontainers/openms-thirdparty
+docker pull biocontainers/pyopenms
 ```
 
 Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) can be found on

diff --git a/docs/introduction.md b/docs/introduction.md
@@ -94,13 +94,26 @@ Get started with installing OpenMS using the installers available for different
 ## Installation on different platforms
 
 ```{tab} GNU/Linux
+
+```bash
 wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Debian-Linux-x86_64.deb
+
+```
+
 ```
 
 ```{tab} Windows
+
+```bash
 wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Win64.exe
 ```
 
+```
+
 ```{tab} macOS
+
+```bash
 wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-macOS.dmg
 ```
+
+```
diff --git a/docs/topp/adding-new-tool-to-topp.md → ...topp-and-utils/adding-new-tool-to-topp.md b/docs/topp/adding-new-tool-to-topp.md → ...topp-and-utils/adding-new-tool-to-topp.md
diff --git a/docs/topp/ini-file-editor.md → docs/topp-and-utils/ini-file-editor.md b/docs/topp/ini-file-editor.md → docs/topp-and-utils/ini-file-editor.md
diff --git a/docs/topp-and-utils/proteomicslfq.md b/docs/topp-and-utils/proteomicslfq.md
@@ -0,0 +1,49 @@
+ProteomicsLFQ
+=============
+
+
+ProteomicsLFQ performs label-free quantification of peptides and proteins.
+
+## Input
+
+- Spectra in mzML format
+- Identifications in idXML or mzIdentML format with posterior error probabilities as score type. To generate those we
+  suggest to run:
+  - PeptideIndexer to annotate target and decoy information.
+  - PSMFeatureExtractor to annotate percolator features.
+  - PercolatorAdapter tool (score_type = 'q-value', -post-processing-tdc).
+  - IDFilter (pep:score = 0.01) to filter PSMs at 1% FDR.
+- An experimental design file:
+
+  ```{seealso}
+  [Experimental Design](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ExperimentalDesign.html) for details.
+  ```
+- A protein database in with appended decoy sequences in FASTA format.
+  (e.g., generated by the [OpenMS DecoyDatabase tool](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/namespaceOpenMS.html)).
+  Processing:
+  ProteomicsLFQ has different methods to extract features: ID-based (targeted only), or both ID-based and untargeted.
+  -  The first method uses targeted feature dectection using RT and m/z information derived from identification data to
+     extract features.
+	 ```{note}
+	 Only identifications found in a particular MS run are used to extract features in the same run. No transfer of IDs
+	 (match between runs) is performed.
+	 ```
+  - The second method adds untargeted feature detection to obtain quantities from unidentified features. Transfer of Ids
+    (match between runs) is performed by transfering feature identifications to coeluting, unidentified features with
+	similar mass and RT in other runs.
+
+## Requantification
+
+Optionally, a requantification step is performed that tries to fill NA values. If a peptide has been quantified in
+more than half of all maps, the peptide is selected for requantification. In that case, the mean observed RT
+(and theoretical m/z) of the peptide is used to perform a second round of targeted extraction.
+
+## Output
+
+Output format are as follows:
+
+- mzTab file with analysis results.
+- MSstats file with analysis results for statistical downstream analysis in MSstats.
+- ConsensusXML file for visualization and further processing in OpenMS.
+
+Potential scripts to perform the search can be found under `src/tests/topp/ProteomicsLFQTestScripts`.
diff --git a/docs/topp/swathwizard.md → docs/topp-and-utils/swathwizard.md b/docs/topp/swathwizard.md → docs/topp-and-utils/swathwizard.md
diff --git a/docs/topp/topp.md → docs/topp-and-utils/topp-and-utils.md b/docs/topp/topp.md → docs/topp-and-utils/topp-and-utils.md
@@ -1,5 +1,5 @@
 TOPP
-===
+====
 
 **TOPP - The OpenMS Proteomics Pipeline** is a pipeline for the analysis of HPLC-MS data. It consists of several small
 applications that can be chained to create analysis pipelines tailored for a specific problem.
@@ -20,3 +20,25 @@ swathwizard
 ```
 
 For advanced documentation on every TOPP tool, see the [OpenMS TOPP API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html).
+
+UTILS
+=====
+
+Besides {term}`TOPP`, OpenMS offers range of other tools. They are not included in {term}`TOPP` as they are not part of
+typical analysis pipelines. A set of command line utilities, similar to {term}`TOPP tools`, mostly used during pipeline
+construction or parameter optimization.
+
+
+```{seealso}
+
+[UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)
+
+```
+
+Let's explore one such utitliy tool:
+
+```{toctree}
+:maxdepth: 1
+
+proteomicslfq
+```
diff --git a/docs/topp/toppas.md → docs/topp-and-utils/toppas.md b/docs/topp/toppas.md → docs/topp-and-utils/toppas.md
diff --git a/docs/topp/toppview.md → docs/topp-and-utils/toppview.md b/docs/topp/toppview.md → docs/topp-and-utils/toppview.md
diff --git a/docs/tutorials/TOPP/display-modes-and-view-options.md b/docs/tutorials/TOPP/display-modes-and-view-options.md
@@ -6,7 +6,7 @@ Display modes determine how intensities are displayed. View options configure th
 
 ![TOPPView Icons](../../images/tutorials/topp/TOPPView_icons.png)
 
-# Display Modes
+## Display Modes
 
 Intensity display modes determine the way peak intensities are displayed.
 
@@ -24,7 +24,7 @@ opened it corresponds to the normal mode.
 
 In this mode the maximum currently displayed intensity is treated as if it was the maximum overall intensity.
 
-# View Options
+## View Options
 
 View options configure the view of the current layer.
 

diff --git a/docs/tutorials/TOPP/peptide-property-prediction.md b/docs/tutorials/TOPP/peptide-property-prediction.md
@@ -1,7 +1,7 @@
 Peptide Property Prediction
 ===========================
 
-You can train a model for retention time prediction as well as for the prediction of proteotypic peptides.
+Train a model for retention time prediction as well as for the prediction of proteotypic peptides.
 
 Two applications has been described in the following publications: Nico Pfeifer, Andreas Leinenbach, Christian G. Huber
 and Oliver Kohlbacher Statistical learning of peptide retention behavior in chromatographic separations: A new

diff --git a/docs/tutorials/TOPP/picking-peaks.md b/docs/tutorials/TOPP/picking-peaks.md
@@ -13,7 +13,7 @@ the approximate `fwhm` of peaks, use the estimation included in the PeakPickerWa
 to `true`. After applying the PeakPickerWavelet, observe which peak width was estimated and used for peak picking in the
 log window.
 
-To estimate the peak width, use the measuring tool ([Action Modes and Their Uses](views-in-toppview.md##action-modes-and-their-uses)) to determine
+To estimate the peak width, use the measuring tool ([Action Modes and Their Uses](views-in-toppview.md#action-modes-and-their-uses)) to determine
 the fwhm of one or several representative peaks.
 
 If the peak picker delivers only a few peaks even though the `peak_with` and `signal_to_noise` parameters are set to

diff --git a/docs/tutorials/TOPP/profile-data-processing.md b/docs/tutorials/TOPP/profile-data-processing.md
@@ -51,9 +51,7 @@ Please notice that this method is still **experimental** since it has not been t
 
   See the `PeakPickerHiRes` class documentation for a parameter list.
 
-## Finding the right parameters for the
-
-NoiseFilters, the BaselineFilter and the PeakPickers
+## Finding the right parameters for the NoiseFilters, the BaselineFilter and the PeakPickers
 
 Finding the right parameters is not trivial. The default parameters will not work on most datasets. In order to find
 good parameters, following this procedure: