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Mass Spectrometry Glossary of Terms

The following is a list of some of the most common terms and abbreviations used in mass spectrometry. It is grouped under various headings to aid quick retrieval. The list has been compiled by Professor Anthony Mallet, University of Greenwich, London.



Mass Spectrometry

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This is the technique in which an instrument is employed to produce ions from atoms or molecules (the source) which are then separated according to their charge-to-mass-ratios (see m/z) (the analyser) and detected.

Sources of Ions

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ApCI (Atmospheric Pressure Chemical Ionisation)
Ionisation by reaction with reagents formed with a plasma discharge in air.
AMS (Accelerator Mass Spectrometry)
A specialist technique in which atomic ions are formed by charge stripping in a very high voltage source, fed from a Van de Graff accelerator. The chosen technique for trace level analysis of the 14C isotope in radiocarbon dating and biological tracer studies.
Californium Fission Ionisation
Ionisation as a result of impact with fission fragments from 252Cf.
CI (Chemical Ionisation)
Ionisation by reaction with gaseous reagents.
DI (Desorption Ionisation)
This is a general term encompassing all forms of direct ionisation from a solid or liquid sample (see FAB, FI, Californium Fission Ionisation).
ESI (Electrospray Ionisation)
Ionisation produced by spraying a sample solution through a conducting capillary tube at a high potential.
EI (Electron Ionisation)
Ionisation in the gas phase by interaction with a beam of electrons.
FAB (Fast Atom Bombardment) (see LSIMS)
Ionisation by impact of a beam of energetic atoms and/or ions from an ion gun onto a liquid matrix and the subsequent transfer of energy from the matrix to the analyte.
FD/FI (Field Desorption/Field Ionisation)
The formation of ions by removal of electrons in a high field.
GDI (Glow Discharge Ionisation)
Ionisation from a solid surface by application of a glow discharge.
ICP-MS (Inductively Coupled Plasma Mass Spectrometry)
Ionisation of elements in a high temperature plasma.
LSIMS (Liquid Surface Ionisation MS) ( see FAB).
MALDI (Matrix Assisted Laser Ionisation)
Ionisation by effect of illumination with a beam of laser generated light onto a matrix containing a small proportion of analyte.
NICI (Negative Ion Chemical Ionisation)
Ionisation as a consequence of capture of an electron in the gaseous phase.
Soft Ionisation
Methods leading to the formation of ions with low internal energies. (see CI, FAB, MALDI, ESI, ApCI)
TI (Thermal Ionisation)
Ionisation induced at high temperatures in a gaseous sample with microwave or an inductively coupled plasma.
TSP (Thermospray Ionisation)
Ionisation from a solution of analyte by passing through a heated tube.


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Linear Analysers

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Single Focussing
A magnetic field alone is used to separate ions according to their m/z ratios (strictly, according to their momenta).
Double Focussing
A combination of electrostatic (E) and magnetic (B) fields is used to compensate for variations in the energies of the ions formed in the source and thence to improve the resolution (qv) of the analyser. (see also forward and reverse geometry).
The term used for the magnetic field.
The term used for the voltage in an electrostatic analyser.
The abbreviation for a quadrupole analyser.
The abbreviation used for an Rf only quadrupole collision chamber.
V (Accelerating Voltage)
The voltage applied to the source to accelerate the ions formed into the analyser.
Magnetic instruments are scanned by varying either the magnetic field or the accelerating voltage.
Linked Scans
Specialised scans where functions of B and E are varied (see below).
The application of a combination of DC and AC voltages to four parallel rods creates a filter through which, on application of the appropriate voltages, only ions of any one defined m/z value can be transmitted. If only an Rf field is applied all ions are transmitted (q)
TOF (Time-of-Flight)
The ions formed are all accelerated by a pulsed potential down an evacuated tube (drift region) and their time of arrival at a detector is determined. This is a function of their m/z values.
Reflectron TOF
The ions passing down a TOF analyser are reflected by an electrostatic mirror; this focusses ions of varying kinetic energy, but identical m/z, leading to higher resolution.
DE TOF (Delayed Extraction Time-of-Flight)
A technique in MALDI-TOF mass spectrometry in which improved resolution is obtained by applying a controlled delay between ion formation and acceleration.
TLF-TOF (Time Lag Focussing-Time-of-Flight)
Another term for DE-TOF.
PSD (Post Source Decay)
Describes the fragmentation processes which occur in TOF in the drift region of the analyser.
Orthogonal TOF
In some recent designs the ion beam is analysed by TOF in a direction orthogonal (at right angles) to its original formation
A small six rod device used to focus a divergent beam of ions.

Trap Analysers

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Ions are pulsed into a three dimensional device where they are stored by a quadrupole field. They can then be ejected at defined m/z values by the application appropriate secondary electric fields.
ICR (Ion Cyclotron Resonance) (FTICR)
The ions are held in a trap by a combination of a static magnetic field and an electrical field. Ions are detected in situ by the electrical impulses the circulating ions create in detector plates placed outside the trap and from these the m/z values of the trapped ions can be calculated. A mathematical operation (See FT Fourier Transform) is applied to convert the frequencies measured to m/z values.
A term which defines the performance of an analyser. This parameter describes the degree to which two ions of adjacent m/z can be distinguished from each other with less than a defined amount of overlap. The latter is often quoted as 10% for sector instruments and 50% for quadrupoles. For isolated peaks the same term can be calculated from the width of the peak at defined heights. (see FWHM).
FWHM (Full Width at Half Height)
The resolution for a 50% valley overlap between peaks of adjacent m/z.

Multi-Analyser Configurations

Forward and Reverse Geometry
Refers to double focussing analysers in which the electrostatic analyser precedes or follows the magnetic analyser.
The use of two analysers to detect precursor ions and their product daughter ions (see Tandem Mass Spectrometry).
Tandem Mass Spectrometry
The use of two analysers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). (see MS/MS)
QqQ, ‘Triple quad’
Two quadrupole mass analysers with an intervening Rf-only quadrupole collision chamber..
Two double focussing instruments with a collision chamber between the two analysers.
Hybrid, EBqQ
Double focussing and quadrupole analysers with an intervening Rf-only quadrupole collision chamber.
Quadrupole and TOF analysers with an Rf-only quadrupole collision chamber.


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Faraday Cup
Detect ion of ions by direct impact on a cylindrical metal cup (specially for high precision isotope ratio work).
Electron Multipliers or Photomultipliers
Detection of ions by production of an amplified electric current, either as a consequence of direct impact of the ion on a surface or following production of a photon from a phosphor followed by a photomultiplier tube.
Array Detectors
Solid state devices which detect ions impacting over a region.
Felgett Advantage
The sensitivity improvement which can be obtained by simultaneous detection of all the ions in a spectrum using an array detector.
Channeltron Detector
Compact form of electron multiplier detector.
Microchannel Plate
Electron multiplier detectors with fast responses and a relatively large area over which ions are detected, in common use in TOF analysers.
Data Systems
Computer based instruments which process and record the detector signals as well as providing control for all the processes involved in operating the instrument.
The analogue signal from the detector is processed by an analogue-to-digital converter in the data system. The centroid is the centre-of-gravity of the digitised signal for an ion. From this the m/z for the ‘stick’ spectrum is calculated.
MCA (Multi Channel Analysis)
A computer generated average of a number of spectral scans using continuum data.

The Spectrum

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u (Unified Atomic Mass Unit)
The symbol for the mass of a particle based on 12C = 12u exactly.
The ratio of charge to mass of the ion detected. z is often unity but can be a larger integer especially in ESI-MS.
Mass Spectrum
A plot of m/z or mass (abscissae) versus the intensity, frequently normalised to 100% for the most intense ion detected (ordinates). This is produced by scanning the analyser to transmit ions (or release them from a trap) for a predefined range of m/z values over a fixed period of time.
Base Peak
The most intense ion detected in the spectrum.
Stick Plot
In its most familiar form the mass spectrum is a histogram, obtained by centroiding the raw continuum data, with the bar height representing the (relative) intensity of the detected ion.
Continuum Spectrum
One displaying the full profile of the detected signals for that ion.
Total Ion Current (TIC)
The sum of the intensities of all the ions detected.
Molecular Ion
The ion formed from the original molecule in the source.
Radical Ion
An ion containing an unpaired electron.
Product Ions, Daughter Ions or Fragment Ions
All terms for ions formed by fragmentation of a precursor ion which may be the molecular ion.
Pseudo-Molecular Ions
Ions formed by FAB or chemical ionisation and other soft ionisation methods, in which the molecular ion may be present with a proton or other cations attached or, for negative ions, with a proton removed.
Most elements are composed of a mixture of isotopes. These will be separated in a mass spectrometer. Atoms or molecules containing such elements will display a cluster of ions reflecting the isotopic composition.
Monoisotopic Ion
The ion containing only the most abundant isotopes. (also called the principal ion).
Nominal Ion Mass
The mass of an ion containing the most abundant isotopes, calculated with nominal atomic weights.
Monoisotopic Ion Mass
The mass of an ion containing the most abundant isotopes, calculated with exact atomic weights.
Average Mass (Mr)
The mass of a particle or molecule of given empirical formula calculated using atomic weights for each element.
Accurate Mass
Isotopes have unique precise masses, a consequence of which is that the elemental composition of any molecule, or fragment of one, can be calculated from its mass if this is sufficiently accurately determined.
SIR (Selected Ion Recording)
In target analysis for defined analytes, the analyser is be operated so as to transmit only the calculated m/z values for the components present.
SIM (Selected Ion Monitoring)
Same as SIR
MS/MS (Mass Spectrometry/Mass Spectrometry)
Analysis of the relationship between a precursor ion and its fragment ion(s) making use of two or more analysers, or an ion trap, and frequently involving CAD.
An alternative term for ion decomposition.
Unimolecular Decomposition
This describes the spontaneous fragmentation of an ion. If this takes place inside the ion source a normal mass spectrum is observed; if the decomposition takes place in a field free region, linked scans and MS/MS configurations can detect this event. (see Metastable ion).
Metastable Ion
One which decomposes into a charged product ion and a neutral species during its transmission through the mass spectrometer.
CAD (Collisionally Activated Decomposition)
The fragmentation of an ion induced by collision with a neutral atom or molecule.
Collision Chamber
A region of relatively high pressure contained in an ion focussing device where CAD takes place.
Daughter (or Product) Ion Scans
Scans in which the product ions formed by decomposition of a parent ion are detected. CAD or unimolecular decomposition may be involved in this.
Parent (or Precursor) Ion Scans
Analysis for all the precursor ions of a defined product ion.
Constant Neutral Loss Scans
Analysis of any ions present which lose a common mass (eg 18 for loss of H2O).
MRM (Multiple Reaction Monitoring)
Used for target analysis. MS/MS in which both analysers are set to monitor specified pairs of parent (precursor) and product ions.
Linked Scans
Specialised multi-analyser scans in which each component is scanned simultaneously with a predefined relationship between the fields applied.
A term used in the case of MS/MS experiments with ion traps where product ion analysis is extended over a number of generations.
FT (Fourier Transform)
The mathematical operation used to convert the signals detected in an ICR mass spectrometer to a set of m/z values.
SWIFT (Stored Waveband Inverse Fourier Transform)
A method used in ion traps to select ions of defined m/z value ranges for excitation in the trap prior to an MS/MS experiment.

Sample Introduction

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GC/MS (Gas Chromatography/Mass Spectrometry)
The linking of mass spectrometry to a gas chromatographic system. The gaseous effluent from a capillary GC column can be introduced directly into the mass spectrometer source.
LC/MS (Liquid Chromatography/Mass Spectrometry)
The linking of the effluent from a liquid chromatographic system to a mass spectrometer.
A device to interface a GC with high carrier gas flow rates to a mass spectrometer.
Momentum Separator
An alternative term for a jet separator.
Direct Probes
Devices whereby samples in condensed phases can be introduced directly into ion sources.
MIMS (Membrane Inlet Mass Spectrometry)
This describes a semi-permeable membrane separator which permits passage of vapour directly to the mass spectrometer ion source.
IRMS (Isotope Ratio Mass Spectrometry)
The use of mass spectrometry to determine accurately ratios of isotopes usually in small amounts of gaseous samples. (see Faraday cup).
Pyrolysis MS
In which a sample is pyrolysed, following which the gaseous products are analysed by MS or by GC/MS.
Particle Beam Inlet
A device which sprays a continuous stream of solvent containing the analytes into a heated chamber. The solvents are removed by heat and pumping and the analyte is passed into the ion source as a stream of very fine particles through a jet or momentum separator.

Additional Resources

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  • The American Society for Mass Spectrometry has published several draft lists of definitions of terms and a recent version can be accessed on the web at http//www.asms.org/
  • Another glossary has been published by Micromass UK Ltd. In its ‘Back to Basics’ series of leaflets.
  • IUPAC recommendations for terms for use in mass spectrometry can be found in Todd JFJ, (1991) Pure and Applied Chemistry vol. 63 pp 1541-1566.