OpenMS Glossary#

A glossary of common terms used throughout OpenMS documentation.


Octadecyl (C18) is an alkyl radical C(18)H(37) derived from an octadecane by removal of one hydrogen atom.

collision-induced dissociation#

Collision-induced dissociation is a MS technique to induce fragmentation of selected ions in the gas phase.

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.

consensus maps#
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 (MS2 or MS3) fragment ions, without comparison to a reference proteome.

electrospray ionization#

Electrospray ionization (ESI) is a technique used in MS to produce ions.


A text-based format for representing nucleotide or amino acid sequences.

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.

high performance liquid chromatography#

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.


Stands for isobaric tags for relative and absolute quantitation.


An advanced workflow editor which OpenMS provides a plugin for.


Liquid chromatography-coupled mass spectrometry.

liquid chromatography coupled tandem mass spectrometry#

See LC-MS and MS2.

liquid chromatography#

An analytical technique used to separate molecules of interest.


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.


Used to identifies peptides in MS2 spectra. Read more about MascotAdapter in the OpenMS API reference documentation.


Mass spectra of a sample from a single fragmentation step.

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.


Multi-stage MS


Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the OpenMS API reference documentation.


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.


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 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.


An interface that allows developers to use OpenMS core library classes and methods.


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. A high resolution MS analyzer.


PepNovo is a de de novo peptide sequencing algorithm for MS2 spectra.

peptide-spectrum match#

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.


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.


A mass filter allowing one mass channel at a time to reach the detector as the mass range is scanned.

stable isotope labeling with amino acids in cell culture#

Stands for Stable isotope labeling using amino acids in cell culture.


Selected reaction monitoring is a MS technique for small molecule analysis.


Stands for sequential acquisition of all theoretical fragment ion spectra.


Tandem Mass Tag (TMT) is a MS based system designed to identify and quantify proteins in different samples.


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.


The OpenMS Pipeline is a set of chainable tools to create pipelines for mass spectrometry analysis.

TOPP tools#

OpenMS provides a number of functions that process MS data called TOPP tools. All TOPP tools are described in the OpenMS API reference documentation.


An assistant for GUI-driven TOPP workflow design. It is recommended to use OpenMS through the KNIME plugins.


TOPPView is a viewer for MS and HPLC-MS data.


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.