glossary fixes: improved descriptions

OpenMS · Dec 3, 2024 · 25c621a · 25c621a
1 parent cab3001
commit 25c621a
Showing 1 changed file with 42 additions and 24 deletions.
diff --git a/docs/source/user_guide/glossary.rst b/docs/source/user_guide/glossary.rst
@@ -7,42 +7,48 @@ A glossary of common terms used throughout OpenMS documentation.
     :sorted:
 
     C18
-    octadecyl
         Octadecyl (C18) is an alkyl radical C(18)H(37) derived from an octadecane by removal of one hydrogen atom.
 
     CID
     collision-induced dissociation
-        Collision-induced dissociation is an MS technique to induce fragmentation of selected ions in the gas phase, which are subjected to a subsequent measurement (see :term:`MS2`).
+        Collision-induced dissociation is an MS technique to induce fragmentation of selected ions in the gas phase,
+        which are subjected to a subsequent measurement (see :term:`MS2`).
 
     consensus features
     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>`_.
+        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>`_.
 
     consensus maps
     consensus map
-        A consensus map is a collection of :term:`consensus features` identified from mass spectra across replicate experiments, usually by combining multiple :term:`feature maps`.
-        One consensus map usually contains 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` identified from mass spectra across replicate experiments,
+        usually by combining multiple :term:`feature maps`.
+        One consensus map usually contains 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>`_.
 
     de novo peptide sequencing
-        A peptide’s amino acid sequence is inferred directly from the precursor peptide mass and tandem
+        A peptide's amino acid sequence is inferred directly from the precursor peptide mass and tandem
         mass spectrum (:term:`MS2` or :term:`MS3`) fragment ions, without comparison to a reference proteome.
 
     electrospray ionization
     ESI
         Electrospray ionization (ESI) is a technique used in MS to produce ions.
 
     FASTA
-        A text-based format for representing nucleotide or amino acid sequences.
+        A text-based file format for representing nucleotide or amino acid sequences.
 
     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).
+        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 :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>`_.
+        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>`_.
 
     high performance liquid chromatography
     HPLC
@@ -52,7 +58,8 @@ A glossary of common terms used throughout OpenMS documentation.
         interacts with the stationary phase.
 
     iTRAQ
-        Isobaric tags for relative and absolute quantitation (iTRAQ) is a MS based multiplexing technique designed to identify and quantify proteins from different samples in one single measurement.
+        Isobaric tags for relative and absolute quantitation (iTRAQ) is a MS based multiplexing technique designed to
+        identify and quantify proteins from different samples in one single measurement.
 
     KNIME
         An advanced workflow editor which OpenMS provides a plugin for.
@@ -71,17 +78,21 @@ A glossary of common terms used throughout OpenMS documentation.
 
     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://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_LuciphorAdapter.html>`__.
 
     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).
+        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.
+        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.
 
     MascotAdapter
-        Used to identify peptides in :term:`MS2` spectra. Read more about MascotAdapter in the `OpenMS API reference documentation <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MascotAdapter.html>`__.
+        Used to identify peptides in :term:`MS2` spectra. Read more about this adapter in the `OpenMS API reference documentation
+        <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MascotAdapter.html>`__.
 
     MSGFPlusAdapter
         Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the
@@ -93,8 +104,8 @@ A glossary of common terms used throughout OpenMS documentation.
 
     MS2
     MS/MS
-    tandem mass spectrometry
-        Tandem MS is a technique where two or more mass analyzers are coupled together using an additional, usually destructive, reaction step to generate fragment ions which increases their abilities to analyse chemical samples.
+        Tandem MS is a technique where two or more mass analyzers are coupled together using an additional, usually destructive,
+        reaction step to generate fragment ions which increases their abilities to analyse chemical samples.
 
     MS3
         Multi-stage MS.
@@ -142,7 +153,8 @@ A glossary of common terms used throughout OpenMS documentation.
         It provides a framework for unified MS data file access and performs standard chemistry and LCMS dataset computations.
 
     quadrupole
-        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.
+        A low resolution MS analyzer.
+        A mass filter allowing one mass channel at a time to reach the detector as the mass range is scanned.
 
     SILAC
     stable isotope labeling with amino acids in cell culture
@@ -152,29 +164,35 @@ A glossary of common terms used throughout OpenMS documentation.
         Selected reaction monitoring (SRM) is a MS technique for targeted small molecule analysis.
 
     SWATH
-        Sequential acquisition of all theoretical fragment ion spectra (SWATH) uses partially overlapping MS2 scans with wide isolation windows to capture all fragment ions in a data independent analysis (DIA).
+        Sequential acquisition of all theoretical fragment ion spectra (SWATH) uses partially overlapping MS2 
+        scans with wide isolation windows to capture all fragment ions in a data independent analysis (DIA).
 
     tandem mass spectrometry
         See :term:`MS2`.
 
     time-of-flight
     TOF
-        Time-of-flight (TOF) is the time taken by an object, particle or wave (be it acoustic, electromagnetic, etc.) to travel a distance through a medium.
+        Time-of-flight (TOF) is the time taken by an object, particle or wave (be it acoustic, electromagnetic, etc.)
+        to travel a distance through a medium.
         TOF analyzers can obtain good, but not ultra-high resolution, such as an :term:`orbitrap`.
 
     TMT
-        Tandem Mass Tag (TMT) is a MS based multiplexing technique designed to identify and quantify proteins from different samples in one single measurement.
+        Tandem Mass Tag (TMT) is a MS based multiplexing technique designed to identify and 
+        quantify proteins from different samples in one single measurement.
 
     TOPP
-       'TOPP - The OpenMS PiPeline' is a pipeline for the analysis of HPLC-MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. See :term:`TOPP tools`.
+       'TOPP - The OpenMS PiPeline' is a pipeline for the analysis of HPLC-MS data. It consists of several small 
+       applications that can be chained to create analysis pipelines tailored for a specific problem. See :term:`TOPP tools`.
 
     TOPPAS
-        An assistant for GUI-driven :term:`TOPP` workflow design, build into OpenMS. See `TOPPAS tutorial <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPPAS_tutorial.html>` for details.
+        An assistant for GUI-driven :term:`TOPP` workflow design, build into OpenMS. 
+        See `TOPPAS tutorial <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPPAS_tutorial.html>` for details.
 
     TOPP tools
         OpenMS provides a number of applications (executable files) that are chainable in a pipeline/script and each process MS data.
         These tools are subdivided into different categories, such as 'File Handling' or 'Peptide Identification'.
-        All :term:`TOPP` tools are described in the `OpenMS API reference documentation <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html>`__.
+        All :term:`TOPP` tools are described in the `OpenMS API reference documentation
+        <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html>`__.
 
     TOPPView
-        TOPPView is a viewer for
+        TOPPView is a viewer for MS and HPLC-MS data and shipped with every OpenMS release.