diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 0e9a51d1..6492fa4e 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,7 +1,7 @@
 <!--
 # openms/openms-docs pull request
 
-Thank you for thinking about contributing to OpenMS Documentation!
+Thank you for contributing to OpenMS Documentation!
 
 Please fill in the appropriate checklist below.
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1465d6fd..36670644 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,13 @@
-OpenMS 2.8.0 Documentation which includes
-
-1. OpenMS Introductory Pages
-2. Installation Instructions
-3. TOPP and TOPPAS tutorials
-4. TOPP Introductory Documentation
-5. User QuickStart Guide
-6. Contacting OpenMS
+------------------------------------------------------------------------------------------
+----                                OpenMS 3.1.0     (released: under development)    ----
+------------------------------------------------------------------------------------------
+
+ - fix some TOPPAS inaccuracies
+
+
+
+------------------------------------------------------------------------------------------
+----                                OpenMS 3.0     (released 7/2023)                  ----
+------------------------------------------------------------------------------------------
+
+ - initial version
\ No newline at end of file
diff --git a/docs/images/introduction/TOPPAS_logo_dark.png b/docs/images/introduction/TOPPAS_logo_dark.png
new file mode 100644
index 00000000..23f962c4
Binary files /dev/null and b/docs/images/introduction/TOPPAS_logo_dark.png differ
diff --git a/docs/images/introduction/TOPPAS_logo_white.png b/docs/images/introduction/TOPPAS_logo_white.png
new file mode 100644
index 00000000..3edd96fb
Binary files /dev/null and b/docs/images/introduction/TOPPAS_logo_white.png differ
diff --git a/docs/index.rst b/docs/index.rst
index 6c633a8c..8dc40596 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -63,6 +63,7 @@ Contents
    run-workflows-with-openms-tools/openms-in-knime.md
    run-workflows-with-openms-tools/openms-in-nextflow.md
    run-workflows-with-openms-tools/openms-on-galaxy.md
+   run-workflows-with-openms-tools/openms-in-toppas.md
 
 .. toctree::
    :maxdepth: 2
diff --git a/docs/openms-applications-and-tools/openms-graphical-user-interfaces.md b/docs/openms-applications-and-tools/openms-graphical-user-interfaces.md
index 1d6628d3..8e89d49d 100644
--- a/docs/openms-applications-and-tools/openms-graphical-user-interfaces.md
+++ b/docs/openms-applications-and-tools/openms-graphical-user-interfaces.md
@@ -11,9 +11,9 @@ OpenMS provides a suite of graphical user interfaces, designed for users who wan
 
   A GUI application used to inspect, visualize and compare mass spectrometry data. For more information, read our [TOPPView: Visualize with OpenMS](visualize-with-openms.md) section.
 
-- **TOPPAS (deprecated)**
+- **TOPPAS**
 
-  A GUI application used to apply multiple tools sequentially on mass spectrometry data. Applying multiple tools in a sequence is referred to as a workflow or a pipeline. OpenMS no longer supports TOPPAS and instead recommends the use of [KNIME](https://www.knime.com/), for which we provide a community plugin.
+  A simple GUI application shipped with OpenMS used to apply multiple TOPP tools sequentially on mass spectrometry data. Applying multiple tools in a sequence is referred to as a workflow or a pipeline. Interacting with external tools (e.g. downstream MSStats) is limited, but all OpenMS TOPP tools are natively supported.
 
 - **SwathWizard**
   An application for SWATH analysis. SwathWizard is used to analyze DIA swath data. For more information, read our [SwathWizard](openms-applications/swathwizard.md) section.
diff --git a/docs/quick-reference/glossary.md b/docs/quick-reference/glossary.md
index f1edc165..6b1ebf11 100644
--- a/docs/quick-reference/glossary.md
+++ b/docs/quick-reference/glossary.md
@@ -72,26 +72,29 @@ collision-induced dissociation (CID)
   induced dissociation.
 
 TOPP
-  The OpenMS Pipeline.
+  The OpenMS Pipeline, see TOPP Tools.
 
 MSGFPlusAdapter
-  Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the [OpenMS API reference documentation](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MSGFPlusAdapter.html).
+  Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the [OpenMS API reference documentation](https://openms.de/current_doxygen/html/TOPP_MSGFPlusAdapter.html).
 
 LuciphorAdapter
   Adapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass
-  spectrometry data. More information is available in the [OpenMS API reference documentation](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_LuciphorAdapter.html).
+  spectrometry data. More information is available in the [OpenMS API reference documentation](https://openms.de/current_doxygen/html/TOPP_LuciphorAdapter.html).
 
 pyOpenMS
   pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and
   metabolomics data in Python. For pyOpenMS documentaion visit [this](https://pyopenms.readthedocs.io/en/latest/) link.
 
 TOPP Tools
-  OpenMS provides a number of functions that process mass spectrometry data called TOPP tools. More information on TOPP tools can be found in the [OpenMS API reference documentation](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html).
+  OpenMS provides a number of programs, called TOPP tools, that process mass spectrometry data. More information on TOPP tools can be found in the [OpenMS API reference documentation](https://openms.de/current_doxygen/html/TOPP_documentation.html).
+
+TOPP tool
+  see {term}`TOPP Tools`
 
 TOPPView
-  TOPPView is a viewer for MS and HPLC-MS data. More information is available in [TOPPView documentation](../openms-applications-and-tools/visualize-with-openms.md).
+  TOPPView is a viewer for MS and HPLC-MS data which ships with OpenMS. More information is available in [TOPPView documentation](../openms-applications-and-tools/visualize-with-openms.md).
 
-[Nightly Snapshot](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html)
+[Nightly Snapshot](https://openms.de/current_doxygen/html/index.html)
   Untested installers and containers are known as the nightly snapshot.
 
 proteomics
@@ -102,7 +105,7 @@ proteins
   muscle to the enzymes that catalyze the digestion of food to synthesizing and replicating DNA.
 
 Mascot
-  Identifies peptides in MS/MS spectra via Mascot. Please find more information in the {term}`TOPP` [Documentation](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MascotAdapter.html).
+  A so-called search engine: It identifies peptide sequences from MS/MS spectra. Please find more information in the {term}`TOPP` [Documentation](https://openms.de/current_doxygen/html/TOPP_MascotAdapter.html).
 
 HPLC-MS
   Data produced by High performance liquid chromatography (HPLC) separates components of a mixture, whereas mass
@@ -124,7 +127,7 @@ spectra
   Plural of spectrum.
 
 mass spectrum
-  A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio. A mass spectrum is produced by a single mass spectrometry run. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. OpenMS represents a one dimensional mass spectrum using the class [MSSpectrum](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1MSSpectrum.html). 
+  A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio. A mass spectrum is produced by a single mass spectrometry run. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. OpenMS represents a one dimensional mass spectrum using the class [MSSpectrum](https://openms.de/current_doxygen/html/classOpenMS_1_1MSSpectrum.html). 
 
 m/z
   mass to charge ratio.
@@ -142,19 +145,19 @@ de novo peptide sequencing
   A peptide’s amino acid sequence is inferred directly from the precursor peptide mass and tandem mass spectrum ({term}`MS/MS` or {term}`MS^3`) fragment ions, without comparison to a reference proteome.
 
 TOPPAS
-  An assistant for GUI-driven TOPP workflow design. It is recommended to use OpenMS through the KNIME plugins.
+  An graphical user interface (GUI), which is shipped with OpenMS, to create and execute worflows using {term}`TOPP tools`; see [TOPPAS tutorial](https://openms.de/current_doxygen/html/TOPPAS_tutorial.html).
 
 chromatogram
-  A two-dimensional plot that describes the amount of analyte eluted from a chromatography versus the analyte's retention time. OpenMS represents a chromatogram using the class [MSChromatogram](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/structOpenMS_1_1Interfaces_1_1Chromatogram.html)
+  A two-dimensional plot that describes the amount of analyte eluted from a chromatography versus the analyte's retention time. OpenMS represents a chromatogram using the class [MSChromatogram](https://openms.de/current_doxygen/html/structOpenMS_1_1Interfaces_1_1Chromatogram.html)
 
 KNIME
   An advanced workflow editor which OpenMS provides a plugin for.
 
 SILAC
-  Stands for Stable isotope labeling using amino acids in cell culture.
+  Stands for 'Stable isotope labeling using amino acids in cell culture'.
 
 iTRAQ
-  Stands for Isobaric tags for relative and absolute quantitation.
+  Stands for 'Isobaric tags for relative and absolute quantitation'.
 
 TMT
   Tandem Mass Tag (TMT) is a mass spectrometry based system designed to identify and quantify proteins in different samples.
@@ -163,7 +166,7 @@ SRM
   Selected reation monitoring is a mass spectrometry technique for small molecule analysis.
 
 SWATH
-  Stands for Sequential acquisition of all theoretical fragment ion spectra.
+  Stands for 'Sequential acquisition of all theoretical fragment ion spectra'.
 
 OpenMS API
   An interface that allows developers to use OpenMS core library classes and methods. 
@@ -174,27 +177,24 @@ RT
 MS
   Mass Spectrometry
 
-TOPP tool
-  OpenMS offers a vast array of TOPP tools for processing, analyzing and visualizing mass spectrometry data.
-
 MS^3
   Multi-stage Mass Spectrometry
 
 feature
-  An LC-MS feature represents the combined isotopic mass traces of a detected chemical compound. The chromatographic peak shape of a feature is defined by the interaction of the analyte with the LC column. Each feature contains information on retention time, mass-to-charge ratio, intensity and overall quality. OpenMS represents a feature using the class [Feature](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1Feature.html).
+  An LC-MS feature represents the combined isotopic mass traces of a detected chemical compound. The chromatographic peak shape of a feature is defined by the interaction of the analyte with the LC column. Each feature contains information on retention time, mass-to-charge ratio, intensity and overall quality. OpenMS represents a feature using the class [Feature](https://openms.de/current_doxygen/html/classOpenMS_1_1Feature.html).
 
 feature map
-  A feature map is a collection of features identified in a mass spectrum from a single experiment. One feature map can contain many features. OpenMS represents a feature map using the class [FeatureMap](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1FeatureMap.html).
+  A feature map is a collection of features identified in a mass spectrum from a single experiment. One feature map can contain many features. OpenMS represents a feature map using the class [FeatureMap](https://openms.de/current_doxygen/html/classOpenMS_1_1FeatureMap.html).
 
 consensus feature
-  Features from replicate experiments with similar retention times and m/z values are linked and considered a consensus feature. A consensus feature contains information on the common retention time and m/z values as well as intensities for each sample. OpenMS represents a consensus feature using the class [ConsensusFeature](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ConsensusFeature.html).
+  Features from replicate experiments with similar retention times and m/z values are linked and considered a consensus feature. A consensus feature contains information on the common retention time and m/z values as well as intensities for each sample. OpenMS represents a consensus feature using the class [ConsensusFeature](https://openms.de/current_doxygen/html/classOpenMS_1_1ConsensusFeature.html).
 
 consensus map
-  A consensus map is a collection of {term}`consensus features <consensus feature>` identified from mass spectra across replicate experiments. One consensus map can contain many consensus features. OpenMS represents a consensus map using the class [ConsensusMap](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ConsensusMap.html).
+  A consensus map is a collection of {term}`consensus features <consensus feature>` identified from mass spectra across replicate experiments. One consensus map can contain many consensus features. OpenMS represents a consensus map using the class [ConsensusMap](https://openms.de/current_doxygen/html/classOpenMS_1_1ConsensusMap.html).
 
 peak
-  A single raw data point in a chromatogram or a mass spectrum. OpenMS represents a peak in a chromatogram using the class [ChromatogramPeak](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ChromatogramPeak.html). OpenMS represents a single, one-dimensional peak in a mass spectrum using the class [PeakID](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1Peak1D.html)
+  A single raw data point in a chromatogram or a mass spectrum. OpenMS represents a peak in a chromatogram using the class [ChromatogramPeak](https://openms.de/current_doxygen/html/classOpenMS_1_1ChromatogramPeak.html). OpenMS represents a single, one-dimensional peak in a mass spectrum using the class [PeakID](https://openms.de/current_doxygen/html/classOpenMS_1_1Peak1D.html)
 
 MSExperiment
-  An OpenMS class used to represent a single mass spectrometry run. [Read the documentation for further information](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1MSExperiment.html).
+  An OpenMS class used to represent a single mass spectrometry run. [Read the documentation for further information](https://openms.de/current_doxygen/html/classOpenMS_1_1MSExperiment.html).
 ```
diff --git a/docs/run-workflows-with-openms-tools/knime/tutorial.md b/docs/run-workflows-with-openms-tools/knime/tutorial.md
index 7e004582..37a7e409 100644
--- a/docs/run-workflows-with-openms-tools/knime/tutorial.md
+++ b/docs/run-workflows-with-openms-tools/knime/tutorial.md
@@ -3062,7 +3062,7 @@ Human Metabolome Database in 2013, Nucleic Acids Res 41(Database issue),D801–7
 
 [^17]: J. Griss, A. R. Jones, T. Sachsenberg, M. Walzer, L. Gatto, J. Hartler, G. G.
 Thallinger, R. M. Salek, C. Steinbeck, N. Neuhauser, J. Cox, S. Neumann, J. Fan,
-F. Reisinger, Q.-W. Xu, N. Del Toro, Y. Perez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, J. A. Vizcaino, and H. Hermjakob, The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience, Mol Cell Proteomics (Jun 2014), <a href="https://www.mcponline.org/article/S1535-9476(20)32821-8/fulltext">doi:10.1074/mcp.O113.036681</a>. 69
+F. Reisinger, Q.-W. Xu, N. Del Toro, Y. Perez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, J. A. Vizcaino, and H. Hermjakob, The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience, Mol Cell Proteomics (Jun 2014), doi:10.1074/mcp.O113.036681. 69
 
 [^18]: S. Böcker, M. C. Letzel, Z. Lipták, and A. Pervukhin, SIRIUS: Decomposing isotope
 patterns for metabolite identification, Bioinformatics 25(2), 218–224 (2009), <a href="https://academic.oup.com/bioinformatics/article/25/2/218/218950">doi:10.1093/bioinformatics/btn603</a>. 75
@@ -3077,7 +3077,7 @@ Acad. Sci. 112(41), 12580–12585 (oct 2015), <a href="https://www.pnas.org/doi/
 OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data, Nature Biotechnology 32(3), 219–223 (Mar. 2014). 83, 87
 
 [^22]: L. C. Gillet, P. Navarro, S. Tate, H. Röst, N. Selevsek, L. Reiter, R. Bonner, and
-R. Aebersold, <a href="https://www.mcponline.org/article/S1535-9476(20)30442-4/fulltext">Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis.</a>, Molecular & Cellular Proteomics 11(6) (June 2012), <a href="https://www.mcponline.org/article/S1535-9476(20)30442-4/fulltext">doi:10.1074/mcp.O111.016717</a>. 83
+R. Aebersold, Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis, Molecular & Cellular Proteomics 11(6) (June 2012), doi:10.1074/mcp.O111.016717, 83
 
 [^23]: A. Bertsch, C. Gröpl, K. Reinert, and O. Kohlbacher, <a href="https://link.springer.com/protocol/10.1007/978-1-60761-987-1_23">OpenMS and TOPP: open source software for LC-MS data analysis.</a>, Methods in molecular biology (Clifton,
 N.J.) 696, 353–367 (2011), <a href="https://link.springer.com/protocol/10.1007/978-1-60761-987-1_23">doi:10.1007/978-1-60761-987-1_23</a>. 83
@@ -3096,8 +3096,8 @@ of mass spectrometry data, J. Biotechnol. 261(February), 142–148 (2017), <a hr
 
 [^27]: E. W. Deutsch, M. Chambers, S. Neumann, F. Levander, P.-A. Binz, J. Shofstahl,
 D. S. Campbell, L. Mendoza, D. Ovelleiro, K. Helsens, L. Martens, R. Aebersold,
-R. L. Moritz, and M.-Y. Brusniak, <a href="https://www.mcponline.org/article/S1535-9476(20)30489-8/fulltext">TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists</a>, Molecular & Cellular Proteomics
-11(4) (Apr. 2012), <a href="https://www.mcponline.org/article/S1535-9476(20)30489-8/fulltext">doi:10.1074/mcp.R111.015040</a>. 84
+R. L. Moritz, and M.-Y. Brusniak, TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists, Molecular & Cellular Proteomics
+11(4) (Apr. 2012), doi:10.1074/mcp.R111.015040, 84
 
 [^28]: C. Escher, L. Reiter, B. MacLean, R. Ossola, F. Herzog, J. Chilton, M. J. MacCoss, and O. Rinner, <a href="https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.201100463">Using iRT, a normalized retention time for more targeted measurement of peptides</a>., Proteomics 12(8), 1111–1121 (Apr. 2012),
 <a href="https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.201100463">doi:10.1002/pmic.201100463</a>. 84
diff --git a/docs/run-workflows-with-openms-tools/openms-in-toppas.md b/docs/run-workflows-with-openms-tools/openms-in-toppas.md
new file mode 100644
index 00000000..176d3b6d
--- /dev/null
+++ b/docs/run-workflows-with-openms-tools/openms-in-toppas.md
@@ -0,0 +1,14 @@
+OpenMS on TOPPAS
+================
+
+TOPPAS is the build-in workflow editor of OpenMS.
+All TOPP tools can be chained, configured and executed.
+
+TOPPAS workflows run on the local machine where TOPPAS is executed and thus only scale according to the hardware at hand. No automatic distribution across a cluster is supported.
+Also, external tools (anything other than OpenMS TOPP tools), can only be called using a special 'GenericWrapper' node. We generally recommend to run only OpenMS-specific tools in TOPPAS
+and hand the resulting data to other tools, or use other workflow systems, such as KNIME which can fully integrate other tools.
+
+The strong point of TOPPAS is that it ships with OpenMS natively, thus requires no extra installation effort.
+It also has a very shallow learning curve, making it very intuitive to create workflows.
+
+See [TOPPAS tutorial](https://openms.de/current_doxygen/html/TOPPAS_tutorial.html) for more details.
\ No newline at end of file
diff --git a/docs/run-workflows-with-openms-tools/recommended-workflow-systems.md b/docs/run-workflows-with-openms-tools/recommended-workflow-systems.md
index ee902bb2..59f06cf4 100644
--- a/docs/run-workflows-with-openms-tools/recommended-workflow-systems.md
+++ b/docs/run-workflows-with-openms-tools/recommended-workflow-systems.md
@@ -2,6 +2,9 @@
 
 Which workflow environment to choose for running OpenMS tools?
 
+You can run OpenMS TOPP tools from the command line using your custom scripts, or use powerful
+workflow systems designed to make workflow creation and maintenance more fun:
+
 :::{card} KNIME
 :img-top: /images/introduction/KNIMELogoTM.svg
 :link: openms-in-knime
@@ -72,4 +75,28 @@ Server and browser-based interactive workflow editor and runner. A public server
 
 Server and browser-based interactive workflow editor and runner. A public server instance can be used for testing and smaller experiments. Provides nice guided tutorials.
 
+
+:::
+
+:::{card} TOPPAS
+:img-top: /images/introduction/TOPPAS_logo_white.png
+:link: openms-in-toppas
+:link-type: doc
+:class-card: only-light
+:class-img-top: halfwidth
+
+OpenMS' build-in workflow system, with limited capabilities but easy to use and tailored to TOPP tools.
+
+:::
+
+:::{card} TOPPAS
+:img-top: /images/introduction/TOPPAS_logo_dark.png
+:link: openms-in-toppas
+:link-type: doc
+:class-card: only-dark
+:class-img-top: halfwidth
+
+OpenMS' build-in workflow system, with limited capabilities but easy to use and tailored to TOPP tools.
+
+
 :::
diff --git a/docs/tutorials-and-quickstart-guides/guides/contributors-quickstart-guide.md b/docs/tutorials-and-quickstart-guides/guides/contributors-quickstart-guide.md
index 87a0e72a..d548dc15 100644
--- a/docs/tutorials-and-quickstart-guides/guides/contributors-quickstart-guide.md
+++ b/docs/tutorials-and-quickstart-guides/guides/contributors-quickstart-guide.md
@@ -61,7 +61,7 @@ Nightly tests run on different platforms. It is recommended to test on different
 This saves time and increases productivity during continuous integration tests.
 ```
 
-Nightly tests: [CDASH](https://cdash.openms.de/index.php?project=OpenMS).
+Nightly tests: [CDASH](https://cdash.seqan.de/index.php?project=OpenMS).
 
 ## Further contributor resources
 
diff --git a/docs/tutorials-and-quickstart-guides/guides/user-quickstart-guide.md b/docs/tutorials-and-quickstart-guides/guides/user-quickstart-guide.md
index 0a1d220b..2728d5db 100644
--- a/docs/tutorials-and-quickstart-guides/guides/user-quickstart-guide.md
+++ b/docs/tutorials-and-quickstart-guides/guides/user-quickstart-guide.md
@@ -2,7 +2,7 @@ User Quickstart Guide
 ====================
 
 Read the User Quickstart guide to gain a brief understanding of key concepts and how to use the tools. For more in-depth
-information, consult [OpenMS API Reference](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html).
+information, consult [OpenMS API Reference](https://openms.de/current_doxygen/).
 
 ## What is OpenMS
 
@@ -21,22 +21,17 @@ Before using OpenMS, become familiar with the following terms:
 |**TOPPAS**          |A graphical workflow design tool that is used to create pipelines from all {term}`TOPP tools`.|
 |**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`. |
 
-```{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`).
-
-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.
+In general TOPP tools are invoked via the command line, directly or indirectly (e.g. via worflow systems such as KNIME, Nextflow, snakemake, or {term}`TOPPAS`).
 
 ## Adapt pipeline parameters
 
 The default parameters of each tool can usually be tweaked to fit the data and improve results.
+Here, we describe how to work with TOPP tools on a command line (irrespective of the operating system) or using TOPPAS workflow system, which is shipped with OpenMS. 
+For [external workflow systems](../../run-workflows-with-openms-tools/recommended-workflow-systems.md), please refer to their documentation.
+
 
 ### Where do you change pipeline parameters?
 
@@ -44,7 +39,7 @@ The default parameters of each tool can usually be tweaked to fit the data and i
                show up once it is selected. All parameters which would be available on the command line and in the INI
 	       file are shown here as well.
 2. **Command line**: Very basic parameters can be set on the command line, e.g. `FileFilter -rt 1000:2000 .....`
-3. Doing 2 for all parameters would create a very long list, thus, use so-called `.ini` files to provide full parameter
+3. Passing all parameters via commandline would create a very long list, thus, use so-called `.ini` files to provide full parameter
    sets to {term}`TOPP tools`. If no INI file is given, default parameters are used. To get a default `.ini` use
 
    `<tool> -write_ini <file>`
diff --git a/docs/tutorials-and-quickstart-guides/openms-user-tutorial.md b/docs/tutorials-and-quickstart-guides/openms-user-tutorial.md
index 9ee5a895..4fa841af 100644
--- a/docs/tutorials-and-quickstart-guides/openms-user-tutorial.md
+++ b/docs/tutorials-and-quickstart-guides/openms-user-tutorial.md
@@ -3061,7 +3061,7 @@ Human Metabolome Database in 2013, Nucleic Acids Res 41(Database issue),D801–7
 
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+F. Reisinger, Q.-W. Xu, N. Del Toro, Y. Perez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, J. A. Vizcaino, and H. Hermjakob, The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience, Mol Cell Proteomics (Jun 2014), doi:10.1074/mcp.O113.036681 . 69
 
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+R. Aebersold, Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis, Molecular & Cellular Proteomics 11(6) (June 2012), doi:10.1074/mcp.O111.016717, 83
 
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+R. L. Moritz, and M.-Y. Brusniak, TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists, Molecular & Cellular Proteomics
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diff --git a/docs/tutorials/KNIME/KNIME-tutorial.md b/docs/tutorials/KNIME/KNIME-tutorial.md
index 808385e6..2addc494 100644
--- a/docs/tutorials/KNIME/KNIME-tutorial.md
+++ b/docs/tutorials/KNIME/KNIME-tutorial.md
@@ -4,8 +4,6 @@ orphan: true
 KNIME Tutorial
 ==============
 
-Users can now use {term}`KNIME` in place of {term}`TOPPAS`; the later will deprecated with no support in near future.
-
 The below image shows an example workflow in {term}`KNIME`.
 
 ![](/images/tutorials/knime/KNIME_screenshot.png)