OpenMS · cbielow · Sep 15, 2023 · Feb 16, 2023 · Sep 14, 2023 · Sep 15, 2023
diff --git 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
@@ -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
diff --git a/docs/images/introduction/TOPPAS_logo_dark.png b/docs/images/introduction/TOPPAS_logo_dark.png
diff --git a/docs/images/introduction/TOPPAS_logo_white.png b/docs/images/introduction/TOPPAS_logo_white.png
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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.
diff --git 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
@@ -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