Merge pull request #210 from SteffenHeu/mrm

add mrm export documentation

Author: SteffenHeu

docs/module_docs/io_mrmtotsv/example-export.png

@@ -0,0 +1,27 @@
+# Export MRMs to TSV
+
+The Export MRMs to TSV module exports MRM-specific metrics to a tsv or csv table.
+An exemplary export is shown below:
+
+![example-export](example-export.png)
+**Figure 1:** Example export result with [Skip missing features](#skip-missing-features) disabled.
+
+## Parameters 
+
+#### Feature lists
+Select the feature lists that shall be exported. 
+
+#### Export file
+
+Select the file to which the export should export to.
+
+
+#### Skip missing features
+
+Select if the export should skip missing features, if a feature was detected in file A but not in file B. An example of the behaviour is shown in the screenshot (Figure 1) above. Here, the [Skip missing features](#skip-missing-features) option was disabled, creating an empty line for the feature of ID 43 in FILE_B. The export contains the ID of the row the feature belongs and was aligned to, but no q1 or q3 masses, no area, no height, and no RT, since the feature was not detected. 
+
+If the [Skip missing features](#skip-missing-features) option is enabled, this line would not exist.
+
+---
+
+{{ git_page_authors }}

docs/module_docs/io_mrmtotsv/mrm-to-tsv.md

@@ -19,3 +19,21 @@ Raw data is import in the usual fashion see [data import](../../module_docs/io/d
 The imported raw data is converted using the [MRM to scans](../../module_docs/mrm_mrmtoscans/mrm-to-scans.md)
 module. This creates pseudo MS1 and MS2 spectra as well as a feature list, which groups the MRM transitions
 by their retention time and precursor ion mass. 
+
+### Set quantifier masses
+mzmine automatically selects the quantifier mass based on the intensity of the MRM transitions and sets the most intense ion as a quantifier. If other ions shall be used as quantifiers, this module allows the selection.
+[mrm-set-quant-mass.md](../../module_docs/mrm_setquant/mrm-set-quant-mass.md)
+
+### Smoothing in retention time dimension (optional)
+Depending on the LC peak shape (i.e. data noisiness), the user can perform smoothing in retention time dimension. 
+
+### Feature resolving
+Feature resolving step enables separation of co-eluting and overlapping chromatography peaks and as such is one of the pivotal steps in data preprocessing. For more detalis on the algorithm used and parameters settings, see the [Local minimum resolver](../../module_docs/featdet_resolver_local_minimum/local-minimum-resolver.md) module.
+
+### Feature alignment
+
+mzmine offers a specific alignment module for MRM data. The [MRM aligner](../../module_docs/align_mrm/mrm-aligner.md) takes the transitions of a feature into account and only allows alignment of features with the same transitions (in default settings). In principle, MRM feature lists can be aligned to HRMS feature lists using the [Join aligner](../../module_docs/align_join_aligner/join_aligner.md). For downsides of this procedure, see the [the MRM aligner documentation](../../module_docs/align_mrm/mrm-aligner.md#mrm-aligner)
+
+---
+
+{{ git_page_authors }}

docs/workflows/mrmworkflow/mrm-workflow.md

@@ -27,6 +27,7 @@ nav:
           - Export to other software: module_docs/io/data-exchange-with-other-software.md
           - Spectral library export: module_docs/io_spectral_library_export/spectral_library_generation.md
           - Export scans (feature list): module_docs/io_scans_feature/export-scans-feature.md
+          - Export MRM to TSV: module_docs/io_mrmtotsv/mrm-to-tsv.md
       #         TODO Add feature list import/export
       - File merging:
           - Raw data files merging: module_docs/featdet_file_merging/raw-files-merging.md
@@ -148,6 +149,7 @@ nav:
       - Batch processing: workflows/batch_processing/batch-processing.md
       - Library generation: workflows/librarygeneration/library_generation.md
       - SIMSEF: workflows/simsef/simsef_workflow.md
+      - MRM workflow: workflows/mrmworkflow/mrm-workflow.md
 
   - Tools:
       - SIMSEF scheduler: module_docs/tools_simsef/simsef.md