OpenMS Glossary

A glossary of common terms used throughout OpenMS documentation.

LC-MS
LCMS

Liquid Chromatography-coupled 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 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.

atom

An atom is the smallest unit of ordinary matter that forms a chemical element.

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 resolution mass spectrometry analyzer.

MS1

First stage to get a spectra. A sample is injected into the mass spectrometer, ionized, accelerated and analyzed by mass spectrometry.

MS2

Tandem mass spectrometry, also MS/MS, a technique where two or more mass analyzers are coupled together. The ions from MS1 spectra are selectively fragmented and analyzed by a second stage of mass spectrometry.

MS3

Multi-stage Mass Spectrometry

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.

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.

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.

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.

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.

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.

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 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.

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.

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 reaction 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

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.

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.

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.

MSExperiment

An OpenMS class (MSExperiment) used to represent a single mass spectrometry run. Read the documentation for further information.