sort glossary for easier maintenance

OpenMS · cbielow · Dec 12, 2024 · Nov 6, 2024 · Nov 12, 2024 · Dec 3, 2024
commit f6bf6a45e67185c37d272438d6bc581c6aaff068
diff --git a/docs/source/user_guide/glossary.rst b/docs/source/user_guide/glossary.rst
@@ -6,11 +6,56 @@ A glossary of common terms used throughout OpenMS documentation.
 .. glossary::
     :sorted:
 
-    peptide-spectrum match
-    PSM
-        A method used in proteomics to identify proteins from a complex mixture. Involves comparing the
-        mass spectra of peptide fragments generated from a protein sample with a database of predicted
-        spectra, in order to identify the protein that produced the observed peptides.
+    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`).
+
+    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>`_.
+
+    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>`_.
+
+    de novo peptide sequencing
+        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.
+
+    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 :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>`_.
+
+    high performance liquid chromatography
+    HPLC
+        In high performance liquid chromatography (HPLC), analytes are dissolved in a pressurized solvent (mobile phase)
+        and pumped through a solid adsorbent material (stationary phase) packed into a
+        capillary column. Physicochemical properties of the analyte determine how strongly it
+        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.
+
+    KNIME
+        An advanced workflow editor which OpenMS provides a plugin for.
 
     LC-MS
     LCMS
@@ -24,37 +69,24 @@ A glossary of common terms used throughout OpenMS documentation.
     LC
         An analytical technique used to separate molecules of interest.
 
-    FASTA
-        A text-based format for representing nucleotide or amino acid sequences.
-
-    C18
-    octadecyl
-        Octadecyl (C18) is an alkyl radical C(18)H(37) derived from an octadecane by removal of one hydrogen atom.
-
-    ESI
-    electrospray ionization
-        Electrospray ionization (ESI) is a technique used in MS to produce ions.
-
-    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 an :term:`orbitrap`.
-
-    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.
-
-    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.
-        An ultra-high resolution MS analyzer, capable of resolving fine-isotope structure.
+    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>`__.
 
     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.
 
+    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>`__.
+
+    MSGFPlusAdapter
+        Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the
+        `OpenMS API reference documentation <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MSGFPlusAdapter.html>`__.
+
     MS1
         Mass spectra of a sample where only precursor ions (i.e. no fragment ions) can be observed.
         Usually MS1 spectra are recorded to select targets for MS2 fragmentation.
@@ -65,114 +97,84 @@ A glossary of common terms used throughout OpenMS documentation.
         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
-
-    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`).
-
-    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`.
+        Multi-stage MS.
 
-    MSGFPlusAdapter
-        Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the
-        `OpenMS API reference documentation <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MSGFPlusAdapter.html>`__.
-
-    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>`__.
-
-    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>`__.
-
-    UTILS
-        [deprecated since OpenMS 3.1] Besides :term:`TOPP tools`, OpenMS offers a range of other tools. They are not included in :term:`TOPP` as they
-        are not part of typical analysis pipelines. Since OpenMS 3.1 all UTILS are :term:`TOPP tools` under the 'Utilities' category.
-
-    TOPPView
-        TOPPView is a viewer for MS and HPLC-MS data and shipped with every OpenMS release.
-
-    nightly snapshot
-        Untested installers and containers which are created regularly between official releases and reflect the current development state.
-
-    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>`__.
-
-    high performance liquid chromatography
-    HPLC
-        In high performance liquid chromatography (HPLC), analytes are dissolved in a pressurized solvent (mobile phase)
-        and pumped through a solid adsorbent material (stationary phase) packed into a
-        capillary column. Physicochemical properties of the analyte determine how strongly it
-        interacts with the stationary phase.
+    mzData
+    mzdata
+        mzData was the first attempt by the Proteomics Standards Initiative (PSI) from the Human Proteome Organization (HUPO)
+        to create a standardized format for MS data. This format is now deprecated, and replaced by mzML.
 
     mzML
     mzml
         The mzML format is an open, XML-based format for mass spectrometer output files, developed by the Proteomics Standard Initiative (PSI)
         with the full participation of vendors and researchers in order to create a single open format that would be supported by all software.
 
-    mzData
-    mzdata
-        mzData was the first attempt by the Proteomics Standards Initiative (PSI) from the Human Proteome Organization (HUPO)
-        to create a standardized format for MS data. This format is now deprecated, and replaced by mzML.
-
     mzXML
     mzxml
         mzXML is an open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for
         Systems Biology. This format is now deprecated, and replaced by mzML.
 
-    ProteoWizard
-        ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses.
-        It provides a framework for unified MS data file access and performs standard chemistry and LCMS dataset computations.
+    nightly snapshot
+        Untested installers and containers which are created regularly between official releases and reflect the current development state.
+
+    octadecyl
+        See :term:`C18`.
+
+    OpenMS API
+        A C++ interface that allows developers to use OpenMS core library classes and methods.
+
+    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.
+        An ultra-high resolution MS analyzer, capable of resolving fine-isotope structure.
+
+    peptide-spectrum match
+    PSM
+        A method used in proteomics to identify proteins from a complex mixture. Involves comparing the
+        mass spectra of peptide fragments generated from a protein sample with a database of predicted
+        spectra, in order to identify the protein that produced the observed peptides.
 
     PepNovo
         PepNovo is a de :term:`de novo peptide sequencing` algorithm for :term:`MS2` spectra.
 
-    de novo peptide sequencing
-        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.
-
-    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.
+    ProteoWizard
+        ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses.
+        It provides a framework for unified MS data file access and performs standard chemistry and LCMS dataset computations.
 
-    KNIME
-        An advanced workflow editor which OpenMS provides a plugin for.
+    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.
 
     SILAC
     stable isotope labeling with amino acids in cell culture
         Stands for Stable isotope labeling using amino acids in cell culture.
 
-    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.
-
-    TMT
-        Tandem Mass Tag (TMT) is a MS based multiplexing technique designed to identify and quantify proteins from different samples in one single measurement.
-
     SRM
         Selected reaction monitoring (SRM) is a MS technique for targeted small molecule analysis.
 
     SWATH
-        Sequential acquisition of all theoretical fragment ion spectra (SWATH) uses parially 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).
 
-    OpenMS API
-        A C++ interface that allows developers to use OpenMS core library classes and methods.
+    tandem mass spectrometry
+        See :term:`MS2`.
 
-    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 :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>`_.
+    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.
+        TOF analyzers can obtain good, but not ultra-high resolution, such as an :term:`orbitrap`.
 
-    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>`_.
+    TMT
+        Tandem Mass Tag (TMT) is a MS based multiplexing technique designed to identify and quantify proteins from different samples in one single measurement.
 
-    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>`_.
+    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`.
+
+    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.
+
+    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>`__.
+
+    TOPPView
+        TOPPView is a viewer for