OpenMS Glossary

A glossary of common terms used throughout OpenMS documentation.

aerosol: An aerosol is a suspension of fine solid particles or liquid droplets in air or another gas.
atom: An atom is the smallest unit of ordinary matter that forms a chemical element.
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.
collision-induced dissociation (CID): A mass spectrometry technique to induce fragmentation of selected ions in the gas phase. Also known as Collision induced dissociation.
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.
consensus map: A consensus map is a collection of 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.
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.
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.
electrospray ionization (ESI): A technique used in mass spectrometry to produce ions.
FASTA format: A text-based format for representing nucleotide or amino acid sequences.
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.
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.
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.
ion: Any atom or group of atoms that bears one or more positive or negative electrical charges. Positively charged are cations, negavtively charged anions.
iTRAQ: Stands for Isobaric tags for relative and absolute quantitation.
KNIME: An advanced workflow editor which OpenMS provides a plugin for.
LC-MS: Liquid Chromatography-Mass Spectrometry.
Liquid chromatography: An analytical technique used to separate molecules of interest.
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.
m/z: mass to charge ratio.
MascotAdapter: Used to identifies peptides in MS/MS spectra. Read more about MascotAdapter in the OpenMS API reference documentation.
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.
mass spectrometry: An analytical technique used to identify and quantify molecules of interest.
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.
MS: Mass Spectrometry
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.
MS^2: See MS/MS.
MS^3: Multi-stage Mass Spectrometry
MSExperiment: An OpenMS class used to represent a single mass spectrometry run. Read the documentation for further information.
MSGFPlusAdapter: Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the OpenMS API reference documentation.
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.
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.
mzXML: mzXML is an open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for Systems Biology.
Nightly Snapshot: Untested installers and containers are known as the nightly snapshot.
octadecyl (C18): An alkyl radical C(18)H(37) derived from an octadecane by removal of one hydrogen atom.
OpenMS API: An interface that allows developers to use OpenMS core library classes and methods.
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.
peak: A single raw data point in a chromatogram or a mass spectrum. OpenMS represents a peak in a chromatogram using the class ChromatogramPeak. OpenMS represents a single, one-dimensional peak in a mass spectrum using the class PeakID.
PepNovo: PepNovo is a de novo sequencing algorithm for MS/MS spectra.
peptides: A short chain of amino acids.
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.
proteomics: Proteomics is the large-scale study of proteins.
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.
pyOpenMS: pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data in Python.
quadrupole mass filters: A mass filter allowing one mass channel at a time to reach the detector as the mass range is scanned.
retention time: retention time (RT) in liquid chromatography, is the time it takes for a separated analyte to move through the stationary phase.
RT: Retention time.
SILAC: Stands for Stable isotope labeling using amino acids in cell culture.
spectra: Plural of spectrum.
SRM: Selected reation monitoring is a mass spectrometry technique for small molecule analysis.
SWATH: Stands for Sequential acquisition of all theoretical fragment ion spectra.
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.
TMT: Tandem Mass Tag (TMT) is a mass spectrometry based system designed to identify and quantify proteins in different samples.
TOPP: The OpenMS Pipeline.
TOPP tool: OpenMS offers a vast array of TOPP tools for processing, analyzing and visualizing mass spectrometry data.
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.
TOPPAS: An assistant for GUI-driven TOPP workflow design. It is recommended to use OpenMS through the KNIME plugins.
TOPPView: TOPPView is a viewer for MS and HPLC-MS data.
UTILS: Besides TOPP tools, 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 API reference documentation.