OpenMS Glossary#
A glossary of common terms used throughout OpenMS documentation.
- OpenMS API#
OpenMS API Reference. The object-oriented OpenMS core library contains over 1,300 classes and is built on modern C++ infrastructure with native compiler support on Windows, Linux and macOS. The classes are representing core concepts in mass spectrometry as well as the corresponding ontologies defined by the Human Proteome Organization Proteomics Standard Initiative (HUPO-PSI).
- Workflow#
A set of over 185 different tools for common mass spectrometric tasks can be accessed by routine users through the KNIME, and Galaxy workflow systems.
- SILAC#
Stable Isotope Labeling by/with Amino acids in Cell culture is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling.
- iTRAQ#
Isobaric Tags for Relative and Absolute Auantitation (iTRAQ) is an isobaric labeling method used in quantitative proteomics by tandem mass spectrometry to determine the amount of proteins from different sources in a single experiment.
- TMT#
A Tandem Mass Tag (TMT) is a chemical label that facilitates sample multiplexing in mass spectrometry (MS)-based quantification and identification of biological macromolecules such as proteins, peptides and nucleic acids.
- SRM#
Selected Reaction Monitoring (SRM), also called Multiple reaction monitoring, (MRM), is a method used in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass spectrometer and an ion product of a fragmentation reaction of the precursor ions is selected in the second mass spectrometer stage for detection.
- SWATH#
SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted proteomics at large scale.
- KNIME#
Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform.
- LC-MS#
Liquid Chromatography(LC) and Mass Spectrometry(MS).
- Peptides#
A short chain of amino acids.
- 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 atom or group of atoms that bears one or more positive or negative electrical charges. Positively charged are cations, negavtively charged anions.
- 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 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 Proteomics Pipeline.
- MSGFPlusAdapter#
Adapter for the MS-GF+ protein identification (database search) engine. More information is available here.
- LuciphorAdapter#
Adapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass spectrometry data. More information is available here.
- pyOpenMS#
pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data in Python. For pyOpenMS documentaion visit this link.
- TOPP Tools#
- UTILS#
Besides TOPP, OpenMS offers a range of other tools. They are not included in TOPP as they are not part of typical analysis pipelines. More information is present in [OpenMS UTILS Documentation)(https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html).
- TOPPView#
TOPPView is a viewer for MS and HPLC-MS data. More information is available in TOPPView documentation.
- 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.
- Mascot#
Identifies peptides in MS/MS spectra via Mascot. Please find more information in the TOPP Documentation.
- 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.[7] 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#
Singluar of spectrum.
- Spectrum#
A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. 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.
- m/z#
mass to charge ratio.
- RT#
Retention time (RT).
- 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.
- OMSSA#
The Open Mass Spectrometry Search Algorithm (OMSSA) is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences.
- PepNovo#
PepNovo is a de novo sequencing algorithm for MS/MS spectra.
- De novo peptide sequencing#
A peptide’s amino acid sequence is inferred directly from the precursor peptide mass and tandem mass spectrum (MS/MS or 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.