Fixes: review comments by @greengypsy

.github/CONTRIBUTING.md

@@ -5,14 +5,14 @@ Hi there!
 
 Thank you for thinking about enhancing OpenMS Documentation further.
 
-Please feel free:
+Please feel free to:
 
-1. Creating a bug report or feature request in OpenMS Documentation, [here](https://github.com/OpenMS/OpenMS-docs/issues).
-2. Creating a pull request in [OpenMS Documentation](https://github.com/OpenMS/OpenMS-docs) with the change you're proposing.
+1. Create a bug report or feature request in OpenMS Documentation, [here](https://github.com/OpenMS/OpenMS-docs/issues).
+2. Create a pull request in [OpenMS Documentation](https://github.com/OpenMS/OpenMS-docs) with the change you're proposing.
 
-If you need help while doing any of these, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/OpenMS).
+For any questions, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/OpenMS).
 
-## Creating a Pull Request
+## Create a Pull Request(PR)
 
 1. Fork this repository.
 2. Add the change in your fork.
@@ -36,13 +36,13 @@ If you need help while doing any of these, drop us a ping in [OpenMS Gitter](htt
 
 ### Images and figures
 
-For images and figures, follow:
+For images and figures:
 
-1. Add screenshot of the window.
+1. Add a screenshot of the window.
 2. In tutorial, align images in center. Other instructions, should have alighment to left.
 3. Please set the size to `500px` of images added in step-by-step guides or instructions.
 
-## OpenMS Documentation Contributors
+## OpenMS documentation contributors
 
 Thank you for your contribution!
 

docs/contact-us.md

@@ -1,14 +1,13 @@
 Contact Us
 =========
 
-To get in touch with us, please follow preferred medium/channel as listed below:
+Contact us:
 
-1. For [user and contributor real time Gitter chat](https://gitter.im/OpenMS/OpenMS).
+1. Using the user and contributor real time [Gitter chat](https://gitter.im/OpenMS/OpenMS).
 2. Drop us an email at user support [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general)
    mailing list.
 3. To stay updated of new versions of OpenMS and releases, subscribe to [openms-announcements mailing list](https://sourceforge.net/projects/open-ms/lists/open-ms-announcements).
-4. In ordered to report a new bug, please create an issue on GitHub [OpenMS](https://github.com/OpenMS/OpenMS/issues)
-   repository.
+4. To report a new bug, create an issue on GitHub [OpenMS](https://github.com/OpenMS/OpenMS/issues) repository.
 
 
-Say hi, on [OpenMS Twitter](https://twitter.com/openmsteam)!
+Say hi on [OpenMS Twitter](https://twitter.com/openmsteam)!

docs/guides/user-guides/user-quickstart-guide.md

@@ -13,28 +13,29 @@ under the three clause BSD licence and runs under Windows, macOS, and Linux oper
 
 ## Background
 
-Before using [OpenMS.org](https://www.openms.de/), you need to be familiar with the following terms:
+Before using OpenMS, become familiar with the following terms:
 
 | Tool and Utilities | Description |
 |--------------------|-------------|
 |**TOPPView**        |A design tool that is used to view and explore LC-MS data, alignments, groups, peptide identifications, and more.|
 |**TOPPAS**          |A graphical workflow design tool that is used to create pipelines from all TOPP tools (and 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 TOPP tools are accessible from a command prompt/shell or via TOPPAS. See also: [TOPP tutorial]() and [TOPP documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_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 TOPP tools are accessible from a command prompt/shell or via TOPPAS. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)|
 |**UTILS**           |Similar to 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)|
 
 ## How to run a Tool
 
-It is recommended to use TOPPAS. A good start are the example pipelines (select **File** > **Open example file** within TOPPAS).
-In parallel read the documentation of the tools (see [TOPP tutorial](), [TOPP documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html)) and the one of TOPPAS ([TOPPAS tutorial](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html)).
+A good start are the example pipelines (select **File** > **Open example file** within TOPPAS).
 
-Alternatively, you can use the command line and call tools directly. In this case you'll probably want to use some type of shell
+Read the documentation of the tools (see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp/topp.md) and the one of TOPPAS ([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.
 
-## Adapting your Pipeline Parameters
+## Adapte pipeline parameters
 
 The default parameters of each tool can usually be tweaked to fit the data and improve results.
 
-### Where do you change them?
+### Where do you change pipeline parameters?
 
 1. **TOPPAS**: Double-click the node of which you want to change the parameters of. A short docu for each parameter will
                show up once it is selected. All parameters which would be available on the command line and in the INI
@@ -47,20 +48,19 @@ 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](), which is another GUI tool shipped with
+   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
    OpenMS and similar to the one build into TOPPAS.
 
 ### How do I feed the INI file to a Tool?
 
 1. **TOPPAS**: Once you changed the parameters of a node and clicked **Ok**, the parameters are in effect. Because
    they are part of the TOPPAS workflow, they are saved together with the workflow.
-2. **Command line** : Simply supply the INI file via the `-ini` flag,
+2. **Command line** : Supply the INI file via the `-ini` flag,
    `<tool> -ini <file>`
 
    e.g. `FileFilter -ini filefilter.ini`
 
-### What parameters require to be changed and to what value?
+### What parameters to set and to what value?
 
-This is tricky and its not possible to give a general answer. In general, read the tool description, change the
-parameters and compare the results using TOPPView if possible. If that does not help, drop us an email on the
-[OpenMS mailing list]() and ask. Please include all the necessary details we need in order to help you.
+The answer is complex, in general, read the tool description, change the parameters and compare the results using
+TOPPView if possible. If that does not help, [contact us](../../contact-us.md). Please include all the necessary details we need in order to help you.

docs/index.rst

@@ -36,7 +36,7 @@ Contents
    introduction
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
    :caption: Getting Started
 
    installations/installation-on-gnu-linux
@@ -45,20 +45,19 @@ Contents
 
 .. toctree::
    :maxdepth: 2
-   :navigation_depth: 4
    :caption: Quick Start Guides
 
    guides/user-guides/user-quickstart-guide
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
    :caption: Tutorials
 
    tutorials/TOPP/TOPP-tutorial
    tutorials/TOPPAS/TOPPAS-tutorial
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
    :caption: OpenMS TOPP Tools
 
    topp/topp.md

docs/introduction.md

@@ -7,14 +7,14 @@ analyses. It offers an infrastructure for rapid development of mass
 spectrometry related software. OpenMS is free software available under the
 three clause BSD license and runs under Windows, macOS, and Linux.
 
-It comes with a vast variety of pre-built and ready-to-use tools for proteomics
+OpenMS has a vast variety of pre-built and ready-to-use tools for proteomics
 and metabolomics data analysis (TOPPTools) as well as powerful 1D, 2D and 3D
 visualization (TOPPView).
 
 OpenMS offers analyses for various quantitation protocols, including label-free
 quantitation, SILAC, iTRAQ, TMT, SRM, SWATH, etc.
 
-It provides built-in algorithms for de-novo identification and database search,
+OpenMS provides built-in algorithms for de-novo identification and database search,
 as well as adapters to other state-of-the art tools like X!Tandem, Mascot,
 OMSSA, etc. It supports easy integration of OpenMS built tools into workflow
 engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and

docs/topp/ini-file-editor.md

@@ -7,4 +7,4 @@ The values can be edited by double-clicking or pressing F2.
 
 The documentation of each value is shown in the text area on the bottom of the widget.
 
-![](../../images/topp/INIFileEditor.png)
+![INIFileEditor](../images/topp/INIFileEditor.png)

docs/topp/swathwizard.md

@@ -16,9 +16,9 @@ both the intermediate files from OpenSWATH (e.g. the XIC data in `.sqMass` forma
 
 This is how the wizard looks like:
 
-![](../../images/topp/SwathWizard.png)
+![SwathWizard](../images/topp/SwathWizard.png)
 
-Schematic of the internal data flow (all tools are called by SwathWizard in the background) can be found in the
+A schematic of the internal data flow (all tools are called by SwathWizard in the background) can be found in the
 [TOPP Documentation: SwathWizard](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_SwathWizard.html).
 
 A recommended test data for the Wizard is the [PASS00779](https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_View?identifier=PASS00779) dataset.

docs/topp/toppas.md

@@ -11,11 +11,11 @@ up and saved, a workflow can also be run without the GUI using the `ExecutePipel
 
 The following figure shows a simple example pipeline that has just been created and executed successfully:
 
-![](../../images/topp/TOPPAS_simple_example.png)
+![TOPPAS simple example](../images/topp/TOPPAS_simple_example.png)
 
-More information about TOPPAS can be found in the [TOPPAS tutorial](../../tutorials/TOPP/TOPPAS-tutorial.md).
+More information about TOPPAS can be found in the [TOPPAS tutorial](../tutorials/TOPP/TOPPAS-tutorial.md).
 
-The command line parameters of this tool are:
+**The command line parameters of this tool are**:
 
 ```
 TOPPAS -- An assistant for GUI-driven TOPP workflow design.

docs/topp/toppview.md

@@ -5,9 +5,9 @@ TOPPView
 file formats. It also supports viewing data from an OpenMS database. The following figure shows two instances of TOPPView
 displaying a HPLC-MS map and a MS raw spectrum:
 
-![](../../images/topp/TOPPView.png)
+![TOPPView](../images/topp/TOPPView.png)
 
-More information about TOPPView can be found in the [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md).
+More information about TOPPView can be found in the [TOPP tutorial](../tutorials/TOPP/TOPP-tutorial.md).
 
 **The command line parameters of this tool are**:
 

docs/tutorials/TOPP/consensus-peptide-identification.md

@@ -11,11 +11,12 @@ In order to improve the identification accuracy, several identification engines
 identification can be calculated from the results. The image below shows an example where Mascot and OMSSA results are
 fed to the **ConsensusID** tool (ConsensusID is currently usable for Mascot, OMSSA and XTandem).
 
-![](../../images/tutorials/topp/TOPP_consensus_id.png)
+![TOPP Consensus ID](../../images/tutorials/topp/TOPP_consensus_id.png)
 
 
 To combine quantitation and identification results:
 
 Protein/peptide identifications can be annotated to quantitation results (featureXML, consensusXML) by the **IDMapper**
 tool. The combined results can then be exported by the **TextExporter** tool:
+
 [Conversion between OpenMS XML formats and text formats](conversion-between-openms-xml-formats-and-text-formats.md).

docs/tutorials/TOPP/data-analysis-in-toppview.md

@@ -4,14 +4,14 @@ Data Analysis in TOPPView
 TOPPView also offers limited data analysis capabilities for single layers, which will be illustrated in the following
 sections. The functionality presented here can be found in the **Tools** menu:
 
-![](../../images/tutorials/topp/TOPPView_tools_menu.png)
+![TOPPView Tools Menu](../../images/tutorials/topp/TOPPView_tools_menu.png)
 
 ## TOPP Tools
 
 Single TOPP tools can be applied to the data of the currently selected layer or to the visible data of the current layer.
 The following example image shows the TOPP tools dialog:
 
-![](../../images/tutorials/topp/TOPPView_tools.png)
+![TOPPView Tools](../../images/tutorials/topp/TOPPView_tools.png)
 
 To apply a TOPP tool, follow the instructions below:
 
@@ -25,7 +25,7 @@ To apply a TOPP tool, follow the instructions below:
 One can access the metadata, the layer is annotated with. This data comprises e.g. contact person, instrument description
 and sample description.
 
-![](../../images/tutorials/topp/MetaDataBrowser.png)
+![Meta Data Browser](../../images/tutorials/topp/MetaDataBrowser.png)
 
 > **_NOTE:_** Identification data, e.g. from a Mascot run, can be annotated to the spectra or features, too. After
 annotation, this data is listed in the metadata.
@@ -35,4 +35,4 @@ annotation, this data is listed in the metadata.
 Statistics about peak/feature intensities and peak meta information can be displayed. For intensities, it is possible to
 display an additional histogram view.
 
-![](../../images/tutorials/topp/TOPPView_statistics.png)
+![TOPPView Statistics](../../images/tutorials/topp/TOPPView_statistics.png)

docs/tutorials/TOPP/display-modes-and-view-options.md

@@ -4,7 +4,7 @@ Display Modes and View Options in TOPPView
 All of the views support several display modes and view options.
 Display modes determine how intensities are displayed. View options configure the view.
 
-![](../../images/tutorials/topp/TOPPView_icons.png)
+![TOPPView Icons](../../images/tutorials/topp/TOPPView_icons.png)
 
 # Display Modes
 

docs/tutorials/TOPP/feature-detection-on-centroided-data.md

@@ -28,4 +28,4 @@ traces, a tolerated mass deviation between isotopic peaks has to be set (`isotop
 The image shows the centroided peak data and the found peptide features. The used parameters can be found in the TOPP
 tools dialog.
 
-![](../../images/tutorials/topp/TOPPView_tools_ff_centroided.png)
+![TOPPView Tools FF\_Centrioided](../../images/tutorials/topp/TOPPView_tools_ff_centroided.png)

docs/tutorials/TOPP/feature-grouping.md

@@ -21,13 +21,13 @@ To differentially quantify the features of an isotope-labeled HPLC-MS map, follo
    - feature quality of feature 2
    - quality measure for the shift (how near is it to the optimal shift)
 
-   ![](../../images/tutorials/topp/TOPP_labeled_quant.png)
+   ![TOPP labeled quant](../../images/tutorials/topp/TOPP_labeled_quant.png)
 
 ## Label-free quantitation
 
 To differentially quantify the features of two or more label-free HPLC-MS map.
 
-![](../../images/tutorials/topp/TOPP_labelfree_quant.png)
+![TOPP labelfree quant](../../images/tutorials/topp/TOPP_labelfree_quant.png)
 
 > **_NOTE:_** This algorithm assumes that the retention time axes of all input maps are very similar. To correct for
 retention time distortions, please have a look at [Map alignment](map-alignment.md).

docs/tutorials/TOPP/general-introduction.md

@@ -73,7 +73,7 @@ command line flag `-help`. Some TOPP tools also have subsections of parameters t
 algorithm. The documentation of these subsections is not displayed with `–help`. It is however displayed in
 **INIFileEditor**.
 
-![](../../images/tutorials/topp/INIFileEditor.png)
+![INIFileEditor](../../images/tutorials/topp/INIFileEditor.png)
 
 In the [INIFileEditor](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_INIFileEditor.html), click on the respective parameter, the documentation of the parameters is displayed in the window at the bottom.
 

docs/tutorials/TOPP/map-alignment.md

@@ -9,7 +9,7 @@ corrects for shifted and scaled retention times, which may result from changes o
 The different **MapAligner** tools take `n` input maps, de-warp them and store the `n` de-warped maps. The following
 image shows the general procedure:
 
-![](../../images/tutorials/topp/TOPP_alignment.png)
+![TOPP Alignment](../../images/tutorials/topp/TOPP_alignment.png)
 
 There are different map alignment tools available. The following table gives a rough overview of them:
 

docs/tutorials/TOPP/picking-peaks.md

@@ -23,4 +23,4 @@ good values, consider changing the advanced parameter `fwhm_lower_bound_factor`
 The following image shows a part of the spectrum with the picked peaks shown in green, the estimated peak width in the
 log window and the measured peak width.
 
-![](../../images/tutorials/topp/TOPPView_tools_pp_picked.png)
+![TOPPView tools pp\_picked](../../images/tutorials/topp/TOPPView_tools_pp_picked.png)

docs/tutorials/TOPP/profile-data-processing.md

@@ -9,7 +9,7 @@ To find all peaks in the profile data:
 2. The now smoothed profile data can be further processed by subtracting the baseline with the **BaselineFilter**.
 3. Then use one of the **PeakPickers** to find all peaks in the baseline-reduced profile data.
 
-![](../../images/tutorials/topp/TOPP_raw_data.png)
+![TOPP raw data](../../images/tutorials/topp/TOPP_raw_data.png)
 
 There are two different smoothing filters: NoiseFilterGaussian and NoiseFilterSGolay. To use the Savitzky Golay filter,
 or the **BaselineFilter** with non equally spaced profile data, e.g. TOF data, you have to generate equally spaced data
@@ -62,4 +62,4 @@ good parameters, following this procedure:
 2. Extract a single scan from the middle of the HPLC gradient (Right click on **scan**).
 3. Experiment with the parameters until you have found the proper settings
 
-You can find the **NoiseFilters**, the **BaselineFilter**, and the **PeakPickers** in **TOPPView** in the menu **Layer** > **Apply TOPP tool**.
+Find the **NoiseFilters**, the **BaselineFilter**, and the **PeakPickers** in **TOPPView** in the menu **Layer** > **Apply TOPP tool**.

docs/tutorials/TOPP/quality-control.md

@@ -12,7 +12,7 @@ then be processed using custom scripts or via the R package (see [github:cbielow
 
 ![](../../images/tutorials/topp/TOPP_qualitycontrol.png)
 
-An example workflow can be found in `OpenMS/share/OpenMS/examples/TOPPAS/QualityControl.toppas`.
+Find an example workflow in `OpenMS/share/OpenMS/examples/TOPPAS/QualityControl.toppas`.
 
 For data from [TOPP Documentation:IsobaricAnalyzer](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html), just provide the consensusXML as input to
 [TOPP Documentation:QualityControl](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_QualityControl.html). No FeatureXMLs or TrafoXMLs are required. The mzML raw file can be added as input though.

docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md

@@ -8,9 +8,10 @@ between different types of filters (green rectangle), the one mainly used is Top
 the length of the structuring element (blue rectangle). The default value is `3` Thomson. Press **Ok** to start the baseline
 subtraction.
 
-![](../../images/tutorials/topp/TOPPView_tools_baseline.png)
+![TOPPView Tools Baseline](../../images/tutorials/topp/TOPPView_tools_baseline.png)
 
-The following image shows a part of the spectrum after baseline filtering as green line, the original raw data is shown
-by the blue line.
+The following image shows:
+- A part of the spectrum after baseline filtering as a green line.
+- The original raw data as a blue line.
 
-![](../../images/tutorials/topp/TOPPView_tools_baseline_filtered.png)
+![TOPPView Tools Baseline Filtered](../../images/tutorials/topp/TOPPView_tools_baseline_filtered.png)

docs/tutorials/TOPP/toppview-introduction.md

@@ -10,4 +10,4 @@ datasets as well as displaying input data and output data of an algorithm togeth
 TOPPView is intended for visual inspection of the data by experimentalists as well as for analysis software by
 developers.
 
-![](../../images/tutorials/topp/TOPPView_parts.png)
+![TOPPView Parts](../../images/tutorials/topp/TOPPView_parts.png)