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Instruments and information

Glossary of mass spectrometry terms



The process of accumulating and storing data received from instrument sensors as they detect the sample. The conversion of analog signals to digital data fies. 

Adduct Ion 

An ion formed by interaction of two species, usually an ion and a molecule, and often within an ion source, to form an ion containing all the constituent atoms of one species as well as an additional atom or atoms.

Atmospheric Pressure Chemical Ionisation

Atmospheric Pressure chemical Ionisation (APCI) In this method of ionization, an aerosol of a sample solution is sprayed at atmospheric pressure into a heated region in which a sharp metal pin held at high potential sustains a corona discharge. The action of the discharge on the solvent creates reagent ions that react with the neutral sample molecules to create protonated ions of the molecule. These ions then pass through a sampling aperture into the mass analyzer of the mass spectrometer.

Atomic Weight

The atomic weight of an element is the weighted average of the naturally occurring stable isotopes of an element.

Automatic Gain Control (AGC) 

In ion trap mass spectrometry, the software used to set the ion injection time to maintain the optimum quantity of ions for each scan. With AGC on the scan function consists of a prescan and an analytical scan. During the prescan the flux of incoming ions is measured and used to determine the optimum ion injection time for the analytical scan. The ion injection time information is then used to scale the resulting values obtained by the analytical scan.



A constant signal produced by the background level of an instrument.

Base Peak 

The peak in the mass spectrum corresponding to the separated ion beam which has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures.  

Broadband excitation 

A characteristic of using single-frequency resonance excitation with ion trap mass spectrometry is that when the product ions are formed, they are not activated, because they have a resonance frequency that is different from the applied frequency. Broadband excitation is a variation of the resonance-excitation method that can be used to activate these product ions thus eliminating [M-H2O]+ ions which are not considered to be useful fragment ions for identification.


Centroid data

Data used to represent mass spectral peaks in terms of two parameters, the centroid (the weighted centre of mass) and the intensity.

Charge State 

The imbalance between the number of protons (in the nuclei of the atoms) and the number of electrons that a molecular moiety possesses. If the moiety possesses more protons than electrons, its charge state is positive; if it possesses more electrons than protons its charge state is negative.

Collision Induced Dissociation (CID) 

In a collision between an ion and a neutral species, a portion of the ion translational energy is converted to internal energy. This internal energy causes dissociation of the ion into smaller fragment ions and can also cause changes in the ion charge. Collision-induced dissociation is common in MS/MS experiments.

Corona Discharge 

Electrical discharge in the region around the corona discharge needle that results in ionization of gas molecules to form a chemical ionization (CI) plasma, which contains CI reagent ions.


Detector Gain

The ratio of the detector output current to the input ion current.

Duty Cycle 

Duty cycle = Ion collection or detection time/total scan time x 100 %

Dwell Time 

The time spent detecting each m/z value.

Dynamic Range 

A measure of the detection range of a detector. The ratio of the largest to smallest detectable signal.


Electron Ionisation (EI)

The process of molecular ionization initiated by the interaction of the gas phase molecule with an energetic electron. The beam of electrons is emitted from a heated metal filament in the source, and the electrons accelerated through a potential difference of 70 V. The collision between the molecule and the electron causes the ejection of an electron from the molecule (M), and produces a radical molecular ion.

Electron Multiplier (EM)

A detection device inside the vacuum of the mass spectrometer that converts the arrivals of ions at its front dynodes into detectable, amplified electron current at the back lead of the device. The overall gain can be as high as 104 – 108. Positive ions exiting from the mass analyzer impact the first dynode surface, and the impact causes the release of several electrons, which are then accelerated through a potential to the next dynode for a repetition of the impact-release process. A cascade of electrons is produced, generating a current that is further amplified and then sampled by an analog-to-digital converter to be recorded.

Electrospray Ionisation (ESI)

A solution containing the molecules of interest is pumped through a metal capillary tube held at high potential. The solution is sprayed from the tube into a chamber held at ground and open to atmospheric pressure. The sample solution spray creates small droplets that carry a charge induced by the needle potential. The droplets in the mist become progressively smaller as the neutral solvent molecules evaporate. The charge is maintained on the surfaces of the droplets, eventually causing an instability that results in the expulsion of solvent-less highly charges ions of the dissolved sample molecules. Multiple protonation can occur to form highly charged sample molecules.


Flow Injection Analysis

A continuous flow of mobile phase is pumped from the LC into the source. Sample is then injected into the flow using an injection valve and passes directly to the source without passing through a column. This is used to optimize the MS conditions for the LC eluent without the time delay and complication of a column.

Fragment Ion 

An electrically charged dissociation product of an ionic fragmentation. Such an ion may dissociate further to produce other electrically charged molecular or atomic moieties of successively lower formula weight.

Full Mass Scan 

The analysis of all ions in the first stage of a quadrupole tandem mass spectrometer.


Hybrid Mass Spectrometer

A mass spectrometer which combines m/z analysers of different types to perform tandem MS.



A continuous stream of sample is passed into the MS source from a syringe. The sample is dissolved in a suitable solvent such as water, methanol or acetonitrile.


An atomic or molecular species having a net positive or negative electric charge.

Ionisation Efficiency 

It is the ratio of the number of ions formed to the number of electrons used.

Ionisation Energy 

This is the minimum energy of excitation of an atom, molecule or molecular moiety M required to remove an electron in order to produce a positive ion.


Atomic forms of elements that contain the same numbers of protons and electrons, but different nubers of neutrons.



A metallic disk with one or more holes to which an electrical potential can be applied. A lens can be used to accelerate or decelerate ions as the ions approach the lens and to focus an ion beam as the beam passes through the lens.

Limit of Detection (LOD) 

The detection limit reflects the smallest flow of sample that gives a signal that can be distinguished from the background noise. The commonly accepted limit of detection is a signal-to-noise ratio of 3.


Mass Spectrometer

An instrument that measures the m/z and relative abundances of ions.

Mass Spectrum 

A spectrum that is obtained when a beam of ions is separated according to the m/z of the ionic species contained within it.

Mass-to-charge Ratio (m/z) 

The x-axis of a plotted mass spectrum is often labeled in units of m/z, where m denotes the mass of the ion (in Daltons) and z represents the total number of charges on the ion (in units of elemental charge).

Mass Selective Axial Ejection

The use of mass selective instability to eject ions of selected m/z values from an ion trap.

Mass Selective Instability 

A method for selective ejection of ions according to their m/z value in an ion trap.

Mathieu Stability Diagram 

A graphical representation for reduced variables that incorporate the values of DC and RF voltages applied either to the four rods of a quadrupole mass filter or to the electrodes of an ion trap. The stability diagram illustrates areas of ion stability and ion instability and designates scan lines for the changes in those voltages so that the device can serve as an ion m/z analyzer.

Matrix Assisted Lazer Desorption Ionisation (MALDI)

Sample molecules are mixed with an excess of an energy-absorbing (usually solid) matrix. The mixture is co-crystallized in a thin film on an inert metal support. Repetitive irradiation of the film with a pulsed laser releases ions from the surface, which are usually accelerated into a time-of-flight mass spectrometer. Since the matrix is usually a solid organic acid, the predominant mode of ionization is protonation of the sample molecule M to form [M+H]+.


In the ion trap, one complete scan is termed a microscan. Several microscans are usually averaged to improve the S/N and produce a ‘scan’.

Molecular Ion 

An ion formed by the removal from (positive ions) or the addition to (negative ions) a molecule of one or more electrons without fragmentation of the molecular structure. The mass of this ion corresponds to the sum of the masses of the most abundant naturally occurring isotopes of various atoms that make up the molecule, with a correction for the masses of the electrons lost or gained.

Molecular Mass 

The molecular mass (abbreviated M) of a substance, frequently referred to by the older term molecular weight and abbreviated as MW, is the mass of one molecule of that substance, relative to the unified atomic mass unit u[1] (equal to 1/12 the mass of one isotope of carbon-12[2]). This is distinct from the relative molecular mass of a molecule, which is the ratio of the mass of that molecule to 1/12 of the mass of carbon 12 and is a dimensionless number. Relative molecular mass is abbreviated to Mr.


This refers to multi-stage MS/MS experiments where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n>2 whereas for a simple triple quadrupole system n=2.


MS in Time 

MS/MS data that is recorded in one mass analyzer in discreet time steps e.g. in an ion trap. Here the specified scan functions are designed and the resultant MS/MS data subsequently recorded in the same device along a descreet timeline.

MS in Space 

MS/MS data that are recorded in sequential mass analyzers, e.g. triple quadrupole. Specific scan functions are designed such that in one section of the instrument pre-determined ions are selected, then dissociated and the resultant ions are then transmitted to another analyzer for data acquisition.

Multiple Reaction Monitoring (MRM) 

Incorrect term (IUPAC) See Selected Reaction Monitoring (SRM)



A design for a miniaturised electrospray ionization source using a pulled and coated glass capillary as the spray tip. The design achieves a flow rate of 20 - 50 nL/min, much lower than the usual electrospray ionization source. 

Negative Ion 

An atom, radical, molecule or molecular moiety in the vapour phase which has gained one or more electrons, acquiring thereby a negative charge.

Neutral Loss 

In an MS/MS experiment, mass selected precursor ions are induced to dissociate into product ions, which are then mass-analyzed by a second analyzer. Both mass analyzers are scanned at the same rate, with a mass offset between them. Therefore, only ions that dissociate by loss of the specified neutral species mass will form a precursor-product ion pair that is passed through to the detector.



An octagonal array of cylindrical rods that acts as an ion transmission device. An RF voltage and DC offset voltage applied to the rods create an electrostatic field that transmits the ions along the axis of the octapole rods.


Positive Ion

This is an electrically charged atom, radical, molecule or molecular moiety which has lost one or more electrons, thereby acquiring a positive charge.

Precursor Ion 

This is an electrically charged molecular moiety which may dissociate to form fragments, one or more of which may be electrically charged, and one or more neutral species. A precursor ion may be a molecular ion or an electrically charged fragment of a molecular ion.

Precursor Ion Scan 

In an MS/MS experiment, the second mass analyzer is set at the mass of the selected product ion, and the first mass analyzer is scanned from that mass upwards. The result is a mass spectrum that contains signals for all the precursor ions that dissociate to that selected product ion.


In QIT mass spectrometry when automatic gain control is active a prescan preceeds every analytical scan to determine the proper analytical ion injection time. It consists of a short (<10 ms) ion injection to determine the ion current.

Protonated Molecule 

Formed by the addition of a proton to the neutral molecule (M), namely [M+H]+.


Quadrupole Ion Trap (QIT)

An arrangement in which ions with a desired range of mass-to-charge ratios are trapped by making them describe stable paths under the influence of a static and a high frequency, electric, quadrupole field.

Quadrupole Mass Filter (QMF)

In the quadrupole mass filter, the application of a particular combination of DC and RF voltages to four parallel metal rods creates a filtering device through which only ions of a defined m/z value are transmitted. Changing the ratio of the voltages changes the m/z value of the ion that is passed through the detector.


Radical Ion

This is an ion containing an unpaired electron, which is thus both an ion and a radical. In mass spectrometry an unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge.

Relative Abundance 

The relative abundance of an ion is the measured intensity for the beam at that designated m/z value. To be precise, ion beams have intensities, and ions have abundances. Relative abundance is a term related to the practice of assigning the most abundant ion in a measured and plotted mass spectrum a relative abundance of 100 % and normalizing all other ion abundances to that value.

Resolution (mass) 

The smallest mass difference Dm between two equal magnitude peaks such that the valley between them is a specified fraction of the peak height.

Resolving Power 

In a mass spectrum, the observed mass divided by the difference between two masses that can be separated: m/Dm. The method by which Dm was obtained and the mass at which the measurement was made should be reported.

Resonance Ejection

A mode of ion ejection in a quadrupole ion trap that relies on a auxillary RF voltage that is applied to the end-cap electrode. The voltage is turned to the secular frequency of a particular ion to eject it.


Sampling Rate

The rate of signal sampling (measurement) within a definite time.


The analysis of all ions leaving the mass spectrometer within a specified range of m/z values.

Selected Ion Monitoring (SIM)

The practice of monitoring and recording ion currents at one or more selected m/z values with time, rather than recording full mass spectra, as sample is introduced into the ion source. Because the detector is integrating signal for a longer time, rather than recording full mass spectra, as sample is introduced into the ion source. The detector is integrating signal for a longer time at the relevant ion so limits of detection can be lowered.

Selected Reaction Monitoring (SRM)

The specific ions of pre-selected precursor ions recorded via multi-stage MS, i.e. the precursor ion(s) must undergo a specific reaction or transformation to be detected.


The proper definition of sensitivity is that of a system response measured per amount of sample placed in the system. It is the slope of the graph for the sample concentration versus the measured signal.

Signal-to-noise (S/N) ratio 

The ratio of the signal height (S) to the noise height (N). The signal height is the baseline corrected peak height. The noise height is the residual difference, r(max)-r(min), from a linear regression anaysis of the baseline noise. The S/N ratio provides an indication of the clarity of the data. It is generally desirable to maximize the S/N ratio as well as the signal.


The physical part of the mass spectrometer where ionization takes place.

Space Charge Effect 

The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time.


Tandem MS

An instrumental arrangement in which ions are subjected to two or more sequential stages (which may be separated spatially or temporally) of analysis according to the mass-to-charge ratio. The study of ions by means of two stages of mass analysis is termed mass spectrometry/mass spectrometry (MS/MS)


Time of Flight (TOF)

An instrument making use of the fact that ions of different mass-to-charge ratio, all with the same initial translational energy, require different times to traverse a given distance in a field free region.

Total Ion Current (TIC) 

The sum of all the separate ion currents carried by the different ions contributing to the spectrum.


The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region.


1. Murray KK, Boyd RK, Eberlin MN, Langley GJ, Li L, Naito Y, Tabet JC. IUPAC Standard Definitions of Terms Relating to Mass Spectrometry, First Public Draft, June 2005.

2. Busch KL. A Glossary for Mass Spectrometry. Mass Spectrometry 17(6S), 2002.   

3. California Institute of Technology

4. ThermoFinnigan LCQ DECA XP; Xcalibur Help Glossary.

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