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Update KNIME Tutorial #225

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Expand Up @@ -4,7 +4,7 @@ orphan: true
Feature Detection on Centroided Data
====================================

To quantify peptide features, TOPP offers the **FeatureFinder** tools. In this section the **FeatureFinderCentroided**
To quantify peptide features, TOPP offers the **FeatureFinder** tools. In this section the `FeatureFinderCentroided`
is used, which works only on centroided data. There are other FeatureFinders available that also work on profile data.

For this example the file `LCMS-centroided.mzML` from the examples data is used (**File** > **Open example data**). In order
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Expand Up @@ -6,7 +6,7 @@ File Handling

## General information about peak and feature maps

For general information about a peak or feature map, use the **FileInfo** tool.
For general information about a peak or feature map, use the `FileInfo` tool.

- It can print RT, m/z and intensity ranges, the overall number of peaks, and the distribution of MS levels.
- It can print a statistical summary of intensities.
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361 changes: 174 additions & 187 deletions docs/run-workflows-with-openms-tools/knime/tutorial.md

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Expand Up @@ -19,7 +19,7 @@ fed to the **ConsensusID** tool (ConsensusID is currently usable for Mascot and

To combine quantitation and identification results:

Protein/peptide identifications can be annotated to quantitation results (featureXML, consensusXML) by the **IDMapper**
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).
52 changes: 26 additions & 26 deletions docs/tutorials-and-quickstart-guides/openms-user-tutorial.md

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Expand Up @@ -110,7 +110,7 @@ If you want a graphical user interface to interact with, then use TOPPView. Foll

1. Go to **File** > **Open file** and open a file by following the prompts.
2. Go to **Tools** > **Apply TOPP tool (whole layer)**.
3. Set **TOPP tool** to **FileInfo** and **output argument** to **out**.
3. Set **TOPP tool** to `FileInfo` and **output argument** to **out**.
4. Load an existing INI file by clicking **Load** and selecting an INI file from the file importer. If you don’t have an INI file, click **Store**, enter a file name and click **OK** to generate an INI file, then click **Load** and load the file.

![apply topp tool to layer](/images/tutorials/toppview/apply-topp-tool-to-layer.png)
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