Mass Spectrometry Glossary of Terms

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  • Published: Jan 8, 2014
  • Channels: Detectors / Base Peak / Proteomics
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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. Any comments, corrections or additions should be sent to 


Mass Spectrometry    back to top 

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    back to top   

   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.

   Electron Capture Ionisation

   An alternative term for NICI.

   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.

   Ion Mobility Spectrometry. 

   Ions at atmospheric pressure in the gas phase are allowed to drift down a tube ('drift tube') under the influence of an electric potential. They separate according to their charge, mass and overall size and shape. This device is frequently coupled to a mass spectrometer analyser for subsequent detection of the ions and for determination of their mass-to-charge ratios. 

   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.

   Analysers    back to top 

   Linear Analysers   

   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    back to top             


   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.

   Mathieu Stability Diagram

   A graphical representation of the values of DC and AC voltages which, when applied to an ion trap, maintains an ion of given m/z value range in a stable trajectory inside the trap.                           


   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  back to top              

   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).

   SID (Surface Induced Decomposition) 

   Fragmentation of an ion by collision with a solid surface placed between two analysers.

   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.

   BE-BE or EB-EB 

   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.

Detectors     back to top         

   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 or time-of-flight analyser.

   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    back to top     

   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. Thomson is the unit for mass-to-charge ratio.          

   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) abundance 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 abundances of all the ions detected.

   Isobaric Ions

   Ions of identical mass but with different atomic compositions.          

   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    back to top     

   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.          

   Nanoflow Electrospray

   Sample introduction into an ESI source from electrically conducting capillary needles with fine (sub 20m) orifices. Low nanolitre/min flow rates operate.

   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     back to top     

  • 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         
  • 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.

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