enhance glossary and links

docs/source/index.rst

@@ -1,13 +1,13 @@
 Summary
 =======
 
-pyOpenMS is an open-source Python library for :term:`mass spectrometry<Mass spectrometry>`, specifically for the analysis of proteomics
+pyOpenMS is an open-source Python library for :term:`mass spectrometry<Mass Spectrometry>`, specifically for the analysis of proteomics
 and metabolomics data in Python. pyOpenMS implements a set of Python bindings to the OpenMS library for computational
-:term:`mass spectrometry<Mass spectrometry>` and is available for Windows, Linux and macOS.
+:term:`mass spectrometry<Mass Spectrometry>` and is available for Windows, Linux and macOS.
 
 pyOpenMS provides functionality that is commonly used in computational mass
 spectrometry. The pyOpenMS package contains Python bindings for a large part of the `OpenMS <https://openms.de>`_
-library for :term:`mass spectrometry<Mass spectrometry>` based proteomics. It thus provides easy access to
+library for :term:`mass spectrometry<Mass Spectrometry>` based proteomics. It thus provides easy access to
 a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis.
 
 pyOpenMS facilitates the execution of common tasks in proteomics (and other fields of mass spectrometry) such as
@@ -20,8 +20,8 @@ pyOpenMS facilitates the execution of common tasks in proteomics (and other fiel
 - Chromatogram analysis (chromatographic peak picking, smoothing, elution profiles and peak scoring for :term:`SRM`/MRM/PRM/:term:`SWATH`/DIA data)
 - Interaction with common tools in proteomics and metabolomics:
 
-  - Search engines such as Comet, Mascot, MSGF+, MSFragger, SpectraST, XTandem
-  - Post-processing tools such as Percolator, MSstats, Fido
+  - Search engines such as Comet, Mascot, MSGF+, MSFragger, SpectraST, Sage
+  - Post-processing tools such as Percolator, MSstats, Epiphany
   - Metabolomics tools such as SIRIUS, CSI:FingerId
 
 

docs/source/user_guide/adduct_detection.rst

@@ -16,7 +16,7 @@ In pyOpenMS, :py:class:`~.MetaboliteFeatureDeconvolution` takes a :term:`feature
 
 | **Suggested follow up step:**
 | The resulting feature map can be exported to a pandas DataFrame with adduct information from the *dc_charge_adducts* feature meta values.
-| Multiple feature maps can be `combined using the feature linking algorithms <feature_linking.html>`_. Each consensus feature will get a new meta value *best ion* based on the most common annotated adduct within the consensus feature group.
+| Multiple :term:`feature maps` can be `combined using the feature linking algorithms <feature_linking.html>`_. Each consensus feature will get a new meta value *best ion* based on the most common annotated adduct within the consensus feature group.
 
 .. code-block:: python
 

docs/source/user_guide/glossary.rst

@@ -38,14 +38,22 @@ A glossary of common terms used throughout OpenMS documentation.
     TOF
     time-of-flight
         Time-of-flight (TOF) is the time taken by an object, particle or wave (be it acoustic, electromagnetic, e.t.c) to travel a distance through a medium.
+        TOF analyzers can obtain good, but not ultra-high resolution, such as :term:`orbitrap`s.
 
     quadrupole
-        A mass filter allowing one mass channel at a time to reach the detector as the mass range is scanned.
+        A mass filter allowing one mass channel at a time to reach the detector as the mass range is scanned. A low resolution MS analyzer.
 
     orbitrap
         In MS, an ion trap mass analyzer consisting of an outer barrel-like electrode and a coaxial inner
         spindle-like electrode that traps ions in an orbital motion around the spindle.
-        A high resolution MS analyzer.
+        An ultra-high resolution MS analyzer, capable of resolving fine-isotope structure.
+
+    Mass Spectrometry
+    MS
+        An analytical technique to measure the mass over charge (m/z) ratio of ions along with their abundance. This gives rise to a mass spectrum (with m/z on the x-axis and abundance on the y-axis).
+        
+    mass spectrum
+        A visual or numerical representation of a measurement from an MS instrument. A spectrum contains (usually many) pairs of mass-over-charge(m/z)+intensity values.
 
     MS1
         Mass spectra of a sample where only precursor ions (i.e. no fragment ions) can be observed.
@@ -150,9 +158,13 @@ A glossary of common terms used throughout OpenMS documentation.
     OpenMS API
         A C++ interface that allows developers to use OpenMS core library classes and methods.
 
+    feature
+    features
+        A feature, in the OpenMS terminology, subsumes all m/z signals originating from a single compound at a certain charge state. This includes the isotope pattern and usually spans multiple spectra in retention time (the elution profile).
+
     feature maps
     feature map
-        A feature map is a collection of features (all signal originating from a single compound at a certain charge state) identified from a single experiment.
+        A feature map is a collection of :term:`feature`s identified from a single experiment.
         One feature map usually contains 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>`_.
 
     consensus features

docs/source/user_guide/untargeted_metabolomics_preprocessing.rst

@@ -1,9 +1,9 @@
 Untargeted Metabolomics Pre-Processing
 ======================================
 
-The universal workflow for untargeted :terM:`metabolomics` always consists of :terM:`feature` detection in the individual MS sample
+The universal workflow for untargeted metabolomics always consists of :term:`feature` detection in the individual MS sample
 files and their linkage to :term:`consensus features` with common m/z and retention time values.
-In addition, there are optional steps such as adduct detection and annotation of :terM:`features` with associated :term:`MS2` spectra.
+In addition, there are optional steps such as adduct detection and annotation of :term:`features` with associated :term:`MS2` spectra.
 
 .. image:: img/metabolomics-preprocessing.png