A glossary of common terms used throughout OpenMS documentation.
.. glossary::
:sorted:
LC-MS
Liquid Chromatography-Mass Spectrometry.
Liquid chromatography
An analytical technique used to separate molecules of interest.
mass spectrometry
An analytical technique used to identify and quantify molecules of interest.
peptides
A short chain of amino acids.
FASTA format
A text-based format for representing nucleotide or amino acid sequences.
octadecyl (C18)
An alkyl radical C(18)H(37) derived from an octadecane by removal of one hydrogen atom.
Mass
Mass is a measure of the amount of matter that an object contains. In comparison to often used term weight, which is a measure of the force of gravity on that object.
ion
Any :term:`atom` or group of atoms that bears one or more positive or negative electrical charges. Positively charged are cations, negavtively charged anions.
electrospray ionization (ESI)
A technique used in mass spectrometry to produce ions.
MS^2
See :term:`MS/MS`.
atom
An atom is the smallest unit of ordinary matter that forms a chemical element.
electrospray ionization
A technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an :term:`aerosol`.
aerosol
An aerosol is a suspension of fine solid particles or liquid droplets in air or another gas.
time-of-flight (TOF)
A measurement of the time taken by an object, particle of wave (be it acoustic, electromagnetic, e.t.c) to travel a distance through a medium.
quadrupole mass filters
A mass filter allowing one mass channel at a time to reach the detector as the mass range is scanned.
orbitrap analyzers
In mass spectrometry, 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 resoltion mass spectrometry analyzer.
MS(1)
First stage to get a spectra. A sample is injected into the mass spectrometer, ionized, accelerated and analyzed by mass spectrometry.
MS(2)
Ions from MS1 spectra are then selectively fragmented and analyzed by a second stage of mass spectrometry (MS2) to
generate the spectra for the ion fragments.
MS/MS
Tandem mass spectrometry, MS^2^, a technique where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples.
collision-induced dissociation (CID)
A mass spectrometry technique to induce fragmentation of selected ions in the gas phase. Also known as Collision
induced dissociation.
TOPP
The OpenMS Pipeline.
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>`_.
pyOpenMS
pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and
metabolomics data in Python.
TOPP tools
OpenMS provides a number of functions that process mass spectrometry data called TOPP tools. All 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>`_.
TOPPView
TOPPView is a viewer for MS and HPLC-MS data.
Nightly Snapshot
Untested installers and containers are known as the nightly snapshot.
proteomics
Proteomics is the large-scale study of proteins.
proteins
Proteins are vital parts of living organisms, with many functions, for example composing the structural fibers of
muscle to the enzymes that catalyze the digestion of food to synthesizing and replicating DNA.
MascotAdapter
Used to identifies peptides in MS/MS 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>`_.
HPLC-MS
Data produced by High performance liquid chromatography (HPLC) separates components of a mixture, whereas mass
spectrometry (MS) offers the detection tools to identify them.
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.
mzData
mzData was the first attempt by the Proteomics Standards Initiative (PSI) from the Human Proteome Organization (HUPO)
to create a standardized format for Mass Spectrometry data. This format is now deprecated, and replaced by mzML.
mzXML
mzXML is an open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for
Systems Biology.
spectra
Plural of spectrum.
mass spectrum
A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio. A mass spectrum is produced by a single mass spectrometry run. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. OpenMS represents a one dimensional mass spectrum using the class `MSSpectrum <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1MSSpectrum.html>`_.
m/z
mass to charge ratio.
retention time
retention time (RT) in liquid chromatography, is the time it takes for a separated analyte to move through the stationary phase.
ProteoWizard
ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses. It provides a framework for unified mass spectrometry data file access and performs standard chemistry and LCMS dataset computations.
PepNovo
PepNovo is a de novo sequencing algorithm for :term:`MS/MS` :term:`spectra`.
de novo peptide sequencing
A peptide’s amino acid sequence is inferred directly from the precursor peptide mass and tandem mass spectrum (:term:`MS/MS` or :term:`MS^3`) fragment ions, without comparison to a reference proteome.
TOPPAS
An assistant for GUI-driven TOPP workflow design. It is recommended to use OpenMS through the KNIME plugins.
chromatogram
A two-dimensional plot that describes the amount of analyte eluted from a chromatography versus the analyte's retention time. OpenMS represents a chromatogram using the class `MSChromatogram <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/structOpenMS_1_1Interfaces_1_1Chromatogram.html>`_.
KNIME
An advanced workflow editor which OpenMS provides a plugin for.
SILAC
Stands for Stable isotope labeling using amino acids in cell culture.
iTRAQ
Stands for Isobaric tags for relative and absolute quantitation.
TMT
Tandem Mass Tag (TMT) is a mass spectrometry based system designed to identify and quantify proteins in different samples.
SRM
Selected reation monitoring is a mass spectrometry technique for small molecule analysis.
SWATH
Stands for Sequential acquisition of all theoretical fragment ion spectra.
OpenMS API
An interface that allows developers to use OpenMS core library classes and methods.
RT
Retention time.
MS
Mass Spectrometry
TOPP tool
OpenMS offers a vast array of TOPP tools for processing, analyzing and visualizing mass spectrometry data.
MS^3
Multi-stage Mass Spectrometry
feature
An LC-MS feature represents the combined isotopic mass traces of a detected chemical compound. The chromatographic peak shape of a feature is defined by the interaction of the analyte with the LC column. Each feature contains information on retention time, mass-to-charge ratio, intensity and overall quality. OpenMS represents a feature using the class `Feature <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1Feature.html>`_.
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>`_.
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 map
A consensus map is a collection of :term:`consensus features <consensus feature>` 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>`_.
peak
A single raw data point in a chromatogram or a mass spectrum. OpenMS represents a peak in a chromatogram using the class `ChromatogramPeak <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ChromatogramPeak.html>`_. OpenMS represents a single, one-dimensional peak in a mass spectrum using the class `PeakID <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1Peak1D.html>`_.
MSExperiment
An OpenMS class used to represent a single mass spectrometry run. `Read the documentation for further information <https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1MSExperiment.html>`_.