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update domain specific terms in glossary
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cbielow committed Aug 27, 2024
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Expand Up @@ -35,14 +35,9 @@ A glossary of common terms used throughout OpenMS documentation.
electrospray ionization
Electrospray ionization (ESI) is a technique used in MS to produce ions.

MS2
MS/MS
tandem mass spectrometry
Tandem MS is a technique where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples.

TOF
time-of-flight
Time-of-flight (TOF) is the time taken by an object, particle of wave (be it acoustic, electromagnetic, e.t.c) 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, e.t.c) to travel a distance through a medium.

quadrupole
A mass filter allowing one mass channel at a time to reach the detector as the mass range is scanned.
Expand All @@ -53,17 +48,23 @@ A glossary of common terms used throughout OpenMS documentation.
A high resolution MS analyzer.

MS1
Mass spectra of a sample from a single fragmentation step.
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.

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.

MS3
Multi-stage MS

CID
collision-induced dissociation
Collision-induced dissociation is a MS technique to induce fragmentation of selected ions in the gas phase.
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
The OpenMS Pipeline is a set of chainable tools to create pipelines for mass spectrometry analysis.
'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`.

MSGFPlusAdapter
Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the
Expand All @@ -74,21 +75,22 @@ A glossary of common terms used throughout OpenMS documentation.
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 functions that process MS data called :term:`TOPP` tools. 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>`__.
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
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. More information is present in `OpenMS API reference documentation <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html>`__.
[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.
TOPPView is a viewer for MS and HPLC-MS data and shipped with every OpenMS release.

nightly snapshot
Untested installers and containers are known as the nightly snapshot.
Untested installers and containers which are created regularly between official releases and reflect the current development state.

MascotAdapter
Used to identifies peptides in 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 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
Expand All @@ -99,8 +101,8 @@ A glossary of common terms used throughout OpenMS documentation.

mzML
mzml
The mzML format is an open, XML-based format for mass spectrometer output files, developed with the full participation
of vendors and researchers in order to create a single open format that would be supported by all software.
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
Expand All @@ -110,7 +112,7 @@ A glossary of common terms used throughout OpenMS documentation.
mzXML
mzxml
mzXML is an open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for
Systems Biology.
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.
Expand All @@ -124,7 +126,7 @@ A glossary of common terms used throughout OpenMS documentation.
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. It is recommended to use OpenMS through the KNIME plugins.
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.

KNIME
An advanced workflow editor which OpenMS provides a plugin for.
Expand All @@ -134,24 +136,24 @@ A glossary of common terms used throughout OpenMS documentation.
Stands for Stable isotope labeling using amino acids in cell culture.

iTRAQ
Stands for isobaric tags for relative and absolute quantitation.
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 system designed to identify and quantify proteins in different samples.
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 is a MS technique for small molecule analysis.
Selected reaction monitoring (SRM) is a MS technique for targeted small molecule analysis.

SWATH
Stands for sequential acquisition of all theoretical fragment ion spectra.
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).

OpenMS API
An interface that allows developers to use OpenMS core library classes and methods.
A C++ interface that allows developers to use OpenMS core library classes and methods.

feature maps
feature map
A feature map is a collection of features identified in a mass spectrum from a single experiment.
One feature map can contain 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>`_.
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.
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
consensus feature
Expand All @@ -160,5 +162,5 @@ A glossary of common terms used throughout OpenMS documentation.

consensus maps
consensus map
A consensus map is a collection of :term:`consensus features` identified from mass spectra across replicate experiments.
One consensus map can contain 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>`_.

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