OpenMS Glossary#
A glossary of common terms used throughout OpenMS documentation.
- C18#
- octadecyl#
Octadecyl (C18) is an alkyl radical C(18)H(37) derived from an octadecane by removal of one hydrogen atom.
- CID#
- 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.
- ESI#
- electrospray ionization#
Electrospray ionization (ESI) is a technique used in MS to produce ions.
- FASTA#
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#
- HPLC#
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.
- iTRAQ#
Stands for isobaric tags for relative and absolute quantitation.
- KNIME#
An advanced workflow editor which OpenMS provides a plugin for.
- LC-MS#
- LCMS#
Liquid chromatography-coupled mass spectrometry.
- LC-MS/MS#
- liquid chromatography coupled tandem mass spectrometry#
- liquid chromatography#
- LC#
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.
- MascotAdapter#
Used to identifies peptides in MS2 spectra. Read more about MascotAdapter in the OpenMS API reference documentation.
- MS1#
Mass spectra of a sample from a single fragmentation step.
- 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.
- MS3#
Multi-stage MS
- MSGFPlusAdapter#
Adapter for the MS-GF+ protein identification (database search) engine. More information is available in the OpenMS API reference documentation.
- mzData#
- mzdata#
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.
- 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#
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.
- OpenMS API#
An interface that allows developers to use OpenMS core library classes and methods.
- orbitrap#
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#
PepNovo is a de de novo peptide sequencing algorithm for MS2 spectra.
- peptide-spectrum match#
- PSM#
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#
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.
- quadrupole#
A mass filter allowing one mass channel at a time to reach the detector as the mass range is scanned.
- SILAC#
- stable isotope labeling with amino acids in cell culture#
Stands for Stable isotope labeling using amino acids in cell culture.
- SRM#
Selected reaction monitoring is a MS technique for small molecule analysis.
- SWATH#
Stands for sequential acquisition of all theoretical fragment ion spectra.
- TMT#
Tandem Mass Tag (TMT) is a MS based system designed to identify and quantify proteins in different 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.
- TOPP#
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.
- 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.