A P P E N D I X B

DEFINITIONS OF TERMS RELATED TO

MASS SPECTROMETRY

For a complete list of definitions, see Sparkman OD. Mass Spectrometry Desk
Reference, 2nd ed. Pittsburgh, PA: Global View Publishing; 2006.
Accurate mass: More correctly, measured accurate mass is an experimen­
tally determined mass of an ion, a radical, or a molecule that allows the
elemental composition to be deduced. For ions with a mass £200, a
measurement to +5 ppm is sufficient for the determination of the elemental
composition. The term measured accurate mass is used when reporting the
mass to some number of decimal places (usually a minimum of three).
A measured mass should be reported with a precision of the measurement.
This term should not be used to describe the mass calculated from published
tables.
Alpha (α) cleavage (a special form of homolytic cleavage): A frag­
mentation (homolytic cleavage) that results from one of the pair of electrons
between the atom attached to the atom with the odd electron and an
adjacent atom that pairs with the odd electron. After fragmentation, the
atom that contains the charge when the ion is formed retains the charge. A
radical is lost as a result of the fragmentation. This fragmentation is homo­
lytic cleavage because it involves the movement of a single electron (see
exact mass).
amu: See dalton.
Atmospheric pressure chemical ionization (APCI): Chemical ioniza­
tion at atmospheric pressure.
Atomic weight (a.k.a. atomic mass): The weighted average of the
mass of the naturally occurring isotopes of an element. The integer
atomic mass of oxygen was an absolute value of 16 by definition. The
chemical atomic mass scale made the determination of the atomic mass of
newly discovered elements easy by forming their oxides. The atomic
mass is used in the calculation of the average mass. Also see nominal mass
and monoisotopic mass.
Average molecular weight (Mr): The mass of a molecule calculated using
the atomic weight of the elements. Also see molecular weight.
Background: A signal in the mass spectrum due to electrical noise of the
instrument or due to chemical noise from instrument contamination,
column bleed, or sample matrix.
Gas Chromatography and Mass Spectrometry  2010 by Academic Press. Inc.
DOI: 10.1016/B978-0-12-373628-4.00038-1 All rights reserved.

421
422 Appendix B

Base peak: The peak in the mass spectrum with the greatest intensity.
Benzylic cleavage: A fragmentation that takes place at the carbon atom
attached to a phenyl group. When the phenyl group is C6H5, the benzylic
cleavage will result in a benzyl ion with a formula of C6 H5 ¼ CHþ 2 , which
can be isomeric with the tropylium ion. Benzylic cleavage is a special case of
homolytic cleavage and is due to the loss of a pi (π) electron, which places
the site of the charge and the radical on the phenyl ring.

Benzylic carbon
H H
R H
H H H
C C
+
+ +

tropylium
ion

Collisionally activated dissociation (CAD): The same process as colli­

sion-induced dissociation (CID).
Collision-induced dissociation (CID): An ion/neutral process in which the
projectile ion impacts a target neutral species. Part of the translational energy of
the ion is converted to internal energy causing subsequent fragmentation.
Chemical ionization (CI): The formation of new ionized species when
gaseous molecules interact with ions. This process may involve the transfer
of an electron, proton, or other charged species between the reactants in an
ion/molecule reaction. CI refers to positive ions, and negative CI is used for
the formation of negative ions through ion/molecule reaction. The process
of negative chemical ionization (NCI) is different than that of electron
capture negative ionization (ECNI). See electron capture ionization and negative
chemical ionization.
dalton (Da): A unit of mass on the atomic scale that is equal to 1/12 the
mass of an atom of 12C, the most abundant naturally occurring isotope of
carbon. A dalton is a synonym for a unified atomic mass unit (u). Prior to the
establishment of the carbon-12 standard for mass on the atomic scale, two
different definitions of oxygen-16 standard were used and the symbol for
atomic mass was amu. This symbol is now considered obsolete.
Dark matter: A mass spectral experiment results in charged particles (ions)
and neutral particles (that are produced by the fragmentation of the initially
formed ion). These neutral particles (radicals and molecules) are referred to
as the neutral losses from the originally formed ion. These neutral losses are
the dark matter of the mass spectrum. The dark matter is determined by
subtracting an m/z value of a peak (usually representing a fragment ion) that
is lower than that of another peak (usually the M+• peak).
Definitions of Terms Related to Mass Spectrometry 423

Detection limit: The detection limit is the smallest amount of analyte that
is put into the mass spectrometer which provides a signal that can be
distinguished from background noise.
EIC: See mass chromatogram.
Electron capture negative-ion (ECN) detection, electron capture
negative ionization (ECNI), or resonance electron capture ioniza­
tion (RECI): Refers to producing negative ions by the reaction of thermal
electrons with molecules in a mass spectrometer. Thermal electrons are
low-energy electrons that have average kinetic energies which are the
same order-of-magnitude as the thermal energy of the molecules that
they are intended to ionize. These terms are the correct terms to describe
the formation of negative ions when an analyte molecule captures a low-
energy electron. This process, which was first reported as a GC/MS technique
by Ralph Dougherty and later by Don Hunt and George Stafford, usually
happens under high-pressure conditions that are similar to those used in
conventional CI. This is probably the reason that this technique is often
incorrectly referred to as negative chemical ionization (NCI); see chemical
ionization and negative chemical ionization. The resulting negative molecular
ions are symbolized as M−•, which indicates an odd-electron negative ion.
The results of electron capture/ionization are as follows.
Resonance electron capture
AB þ e− ð∼0:1eVÞ→AB−•
Dissociative electron capture
AB þ e− ð0−15eVÞ→A• þB−
Ion-pair formation that results from electron capture
AB þ e− ð>10eVÞ→A− þBþ þ e
Electron ionization (EI): Ionization of analyte molecules in the gas phase
(10−1–10−4 Pa) by electrons accelerated between 50 V and 100 V. The
original standard was 70 V. Ionization by electrons is according to the
following reaction: M + e− → M+• + 2e−. The term electron impact is obsolete
and should not be used.
Electron volt (eV): The unit of energy used to describe the fragmentation
of an ion. An electron volt is a unit of energy that is the work done on an
electron when passing through a potential rise of 1 V. 1 eV = 1.602  10−19 J.
The energy of the electron beam in EI mass spectrometry is expressed in
electron volt. In modern instruments, the ionization energy standard for EI
mass spectrometry is 50–100 eV (i.e., electrons are accelerated between 50 V
and 100 V in the ion source). In the early days of mass spectrometry, the
standard was set at 70 eV; and standard EI is still said to be carried out at 70 eV
resulting in 70-eV spectra. One electron volt is equivalent to 23 kcal of energy.
424 Appendix B

Electrostatic analyzer (ESA): A velocity-focusing device for producing

an electrostatic field perpendicular to the direction of ion travel. Ions of a
given kinetic energy are brought to a common focus. This analyzer is used
in combination with a magnetic analyzer to increase resolution and mass
accuracy.
Elemental composition (EC): A chemical formula stating the number of
atoms of the various elements in a molecule, radical, or ion.
Exact mass: More correctly, the calculated exact mass is the mass determined
by summing the mass of the individual isotopes that compose a single ion, a
radical, or a molecule based on a single mass unit being equal to 1/12 the mass of
the most abundant naturally occurring stable isotope of carbon. The exact mass
values used for the isotopes of each element are recorded in tables of isotopes. The
mass (atomic mass) of an element that appears in the periodic table is a weighted
average of these exact mass values of the naturally occurring stable isotopes of that
element. If the mass is calculated with the exact mass value of the most abundant
naturally occurring stable isotope of each element in the ion, radical, or molecule,
then the calculated exact mass is the same as the monoisotopic mass.
Extracted ion chromatogram or profile (EIC or EIP): See mass
chromatogram.
eV: See electron volt.
FC-43: See perfluorotributylamine.
Field ionization (FI): A soft ionization technique sometimes used in
GC/MS that results in a high abundance of low-energy molecular ions.
Ionization of an analyte molecule in the vapor phase takes place in an
electrical field (107–108 V cm−1) maintained between two sharp points or
edges of two electrodes.
Fragmentation pattern: The result of the decomposition of an ion
(usually the molecular ion in GC/MS) to produce a series of fragment
ions with specific abundances. This pattern is displayed as a mass
spectrum and is a mass spectral graphic presentation of the analyte.
Fragment ion: An ion formed from a charged species representing an
intact molecule. The formation of a fragment ion is unimolecular and results
in a charged species and a neutral, which is either a radical or a molecule.
GC/MS interface: An interface between a gas chromatograph and a mass
spectometer that provides a continuous introduction of eluant gas to the
mass spectometer ion source.
Gamma (γ)-hydrogen shift-induced beta (β) cleavage (a.k.a. the
McLafferty rearrangement): A rearrangement reaction that was originally
described by an Australian chemist, A.J.C. Nicholson (Nicholson 1954), but
was named after F.W. McLafferty (McLafferty 1993) because of the extent
to which he studied and reported the reaction in a wide variety of com­
pound types. An odd-electron fragment ion is formed by the loss of a
molecule. This fragment results from a γ-hydrogen shift to an unsaturated
group such as a carbonyl (when the site of the odd electron and the charge is
Definitions of Terms Related to Mass Spectrometry 425

on the oxygen atom). The γ-hydrogen shift causes the radical site to move
to the carbon atom that originally contained the γ-hydrogen. This new
location of the radical site initiates a cleavage reaction that causes the
fragmentation of the carbon–carbon bond that is beta to the unsaturated
group and the loss of a terminal olefin.
R H +
C O R H +
H C O
H
C and
H2C C
R′ H2C R′

Heterolytic (a.k.a. charge-site-driven or inductive, i) cleavage: A frag­

mentation that results from the pair of electrons between the atom attached to
the atom with the charge and an adjacent atom that moves to the site of the
charge. This fragmentation involves the movement of the charge site to the
adjacent atom. A radical is lost as a result of the fragmentation. The movement
of a pair of electrons is symbolized by a double-barbed arrow

Homolytic cleavage: A fragmentation that results from one of a pair of

electrons between two atoms moving to form a pair with the odd electron.
After fragmentation, the atom that contains the charge when the ion is
formed retains the charge. A radical is lost as a result of the fragmentation.
This reaction involves the movement of a single electron and is symbolized
by a single-barbed arrow, the so-called “fishhook” convention.

Hydride shift: The movement of a hydrogen proton with the two elec­
trons that attach it to an adjacent atom. This movement results in a bond
being broken and a new bond being formed.

.+ Loss of H3C
CH2 Loss of +
N . CH2CH3 C +N CH2
CH CH2
H2N CH2
H H H
CH3
A hydride shift

Hydrogen shift: The movement of a hydrogen atom, usually in response

to a radical site. A hydrogen shift results in a hydrogen proton and one of
the two electrons in the bond between the hydrogen and an adjacent atom
moving away from the ion to another location on the ion. A bond is
broken, and a bond is formed.
426 Appendix B

Ion abundance: Refers to the number of ions present. Ions are found in
mass spectrometers and not on mass spectra. Ion abundance is not a synonym
for peak intensity.
Ion cyclotron resonance (ICR) analyzer: A device to determine the
mass-to-charge ratio of an ion in a magnetic field by measuring its cyclotron
frequency.
Ionization: A process that produces an ion from a neutral atom or
molecule.
Ion series: A series of peaks in an EI mass spectrum that indicate structural
moieties such as a series of peaks spaced 14 m/z units apart, indicating the
presence of an alkyl moiety. Each of the peaks represents carbenium ions
that differ in structure by a single –CH2– group. The starting m/z value of
the series can be a clue to the compound type; e.g., m/z 31 with a succession
of peaks, each 14 m/z units higher than the previous, indicates substitute
aliphatic alcohols. An ion series can be useful in determining the type of a
compound. Another ion series is that associated with an aromatic com­
pound (39, 51, 65, 77, 91, etc.).
Ion trap analyzer (a.k.a. quadrupole ion trap, QIT): A mass-resonance
analyzer that produces a three-dimensional rotationally symmetric quadru­
pole field capable of storing ions at selected mass-to-charge ratios.
Isotope: An atom of an element that differs from other atoms of that
element in the number of neutrons in its nucleus.
Isotope peak: A peak that represents an ion that has the same elemental
composition as the monoisotopic ion but has one or more atoms of one or
more of its elements that are a higher mass isotope. Also see monoisotopic peak.
Isotopic ion: An ion containing one or more of the less abundant naturally
occurring isotopes of the elements that make up the structure.
MS/MS (mass spectrometry/mass spectrometry): A process by which a
stable ion is collisionally activated so that it will undergo fragmentation. This is
done to gain specificity or to learn more about the structure of an ion of a
specific m/z value. MS/MS is sometimes referred to as tandem mass spectrometry.
MW: See molecular weight.
Magnetic analyzer: A direction-focusing device that produces a magnetic
field perpendicular to the direction of ion travel. All ions of a given momen­
tum with the same mass-to-charge ratio are brought to a common focus.
Mass chromatogram (a.k.a. reconstructed or extracted ion current
(RIC or EIC) chromatogram or profile): A display of a data set from a
GC-MS prepared by plotting the ion current from an individual ion, a small
series of m/z values, or the sum of a series of noncontiguous m/z values
versus the record (spectrum) number.
Mass defect: The difference between the integer mass of an atom, ion, radical,
or molecules and its exact mass. Mass defect due to hydrogen can be a factor for
ions that have a mass >500 Da. A negative value for mass defect due to multiple
Cl and/or Br atoms can also be a factor.
Definitions of Terms Related to Mass Spectrometry 427

Mass discrimination: The attribute of an m/z analyzer resulting in the

transition or detection of ions of one m/z value more efficiently than
another. An instrument can exhibit either high- or low-mass discrimination.
Mass discrimination can be due to instrument design or the contamination
condition of the instrument.
Mass spectrometer: An instrument used to separate ions according to their
mass-to-charge ratios and to determine the abundance of ions.
Mass spectrum (also known as spectrum): The data display from a mass
spectrometer. The mass spectrum can be displayed graphically or as
numerically as a series of m/z values paired with an absolute or relative
intensity.
Mass-to-charge ratio (m/z): An abbreviation for division of the observed
mass of an ion by the number of charges the ion carries. Thus, C6H+•6 has m/z
78, but C6H2+•6 has m/z 39.
Metastable ion: An ion that dissociates into a production and a neutral
product during the flight from the ion source to the detector. Metastable
ions can be observed when they occur in a field-free region of the mass
spectometer.
millibar (mbar): See pascal.
Molecular ion: An ion formed by the addition (M−•) or removal (M+•) of
an electron from a molecule without fragmentation. All molecular ions are
odd-electron ions; i.e., they have an odd number of electrons.
Molecular weight (MW): In mass spectrometry, this term is used to refer
to the nominal mass or the monoisotopic mass of a molecule. It is not based
on the atomic weights of the elements but rather on the masses of the most
abundant naturally occurring isotopes of the elements. Also see average
molecular weight. In this book, the symbol “MW” means the nominal mass
of a molecule.
Monoisotopic mass: The mass of an ion calculated using the exact mass of
the most abundant isotope of each element in the formula (e.g., C = 12.0000;
O = 15.9949).
Monoisotopic peak: A peak representing an ion where only a single
isotope of any element is present, and the isotope for each element is the
most abundant naturally occurring isotope.
Negative chemical ionization (NCI): Formation of an ion with a negative
charge using negatively charged reagent ions. The resulting negative ions are
usually adducted ions like RCl−. See chemical ionization.
Neutral loss: Describes the nonionic product of a fragmentation. The
neutral losses are inferred by the mass spectrum rather than explicitly stated.
The mass of a neutral loss (radical or molecule) is determined by the
subtraction of the m/z values of two related mass spectral peaks.
Nominal mass: The mass calculated for an ion when using the integer
mass values of the most abundant naturally occurring isotope of each
element in the formula (e.g., C = 12, O = 16, S = 32, etc.).
428 Appendix B

Nominal mass peak: A monoisotopic peak reported as an integer mass

based on the nominal masses of all the atoms comprising the ion.
PFK: See perfluorokerosene.
pascal (Pa): The derived SI unit of pressure, equal to 1 newton (the force
required to accelerate a standard kilogram at a rate of 1 m sec2 over a
frictionless surface) per square meter. Many mass spectrometry applications
refer to pressure in torr. 1 Torr = ∼133 Pa. The unit millibar (mbar, 10−3
bar) is equal to exactly 100 Pa.
Peak: Perhaps the most confusing term in GC/MS. There are chroma­
tographic peaks; or, to be more specific, there are reconstructed
chromatographic peaks; and there are mass spectral peaks. In GC/MS,
chromatographic peaks are usually depicted as vertical lines; however,
the chromatographic peak has a width (representing the energy disper­
sion of a monoisotopic ion, the minimum and maximum m/z values of
ions that cannot be resolved by the instrument, or both) and a height,
which is directly proportional to the ion current being represented. Care
must always be taken when using the word peak to make sure it is clear
whether a chromatographic peak or a mass spectral peak is meant.
Peak intensity: Refers to the height of a peak on a mass spectrum. The
peak intensity may be expressed in terms of signal strength or relative
intensity (relative to the base peak or a specified peak on the mass spectrum).
Peak intensity is not a synonym for ion abundance. Peaks have intensities,
and ions have abundances.
Precursor ion: An ion that undergoes fragmentation to produce a product
ion and a neutral product in an MS/MS experiment. The term precursor ion
should not be used as a synonym for molecular ion. The term parent ion
should not be used as a synonym for precursor ion.
Perfluorokerosene (PFK): A volatile mixture of aliphatic hydrocarbons
where all the hydrogen atoms have been replaced with fluorine atoms used
for tuning and calibration of the m/z scale of double-focusing mass spectro­
meters. Ions formed by PFK are used in peak matching for accurate mass
assignments.
Perfluorotributylamine: A volatile organic compound used in EI for
tuning to calibrate the m/z scale of quadrupole and quadrupole ion trap
mass spectrometers. It has the following structure:
F
F
F F
F
F
F F
F F F F
F F F F
F N F F

F F F F
F F F F
Definitions of Terms Related to Mass Spectrometry 429

Product ion: An ion related to a precursor ion by a process such as

fragmentation in an MS/MS experiment.
QIT: See ion trap analyzer.
QMF: See quadrupole m/z analyzer.
Quadrupole m/z analyzer: A mass filter (QMF) that creates a quadru­
pole field with dc and rf components so that only ions of a selected
m/z value are transmitted to the detector.
RIC: See mass chromatogram.
Radical ion (odd electron ion): An ion containing an unpaired
electron that is both a radical and an ion.
Rearrangement ion: A dissociation product ion in which atoms or groups
of atoms have transferred positions in the original ion during the
fragmentation process. This usually involves the loss of a molecule.
Reconstructed ion chromatogram or profile (RIC): See mass
chromatogram.
Resolution: The difference in m/z values of two ions that can just be
separated (Δm). This is based on the same definition used for resolving
power (see resolving power).
Resolving power (10% valley definition): Let two monoisotopic
peaks of equal height in a mass spectrum at masses m and (m – Δm)
be separated by a valley that at its lowest point is 10% of the height of
the peaks. The resolving power (R) is equal to m/Δm.
Resolving power (FWHM): It is not always possible to have two mono-
isotopic peaks of equal intensity; therefore, R can be calculated by measur­
ing the full width of a monoisotopic peak at half its maximum in m/z units.
R calculated in this way is usually 2 the value obtained using the 10%
valley method.
Scan: A term, more often than not, inappropriately (QIT and time-of­
flight (TOF) mass spectrometers are not scanning instruments) used as a
synonym for spectrum or mass spectrum.
Selected ion monitoring (SIM): Describes the operation of a mass
spectometer in which the ion currents of one or several selected m/z
values are recorded, rather than the entire mass spectrum.
Selected reaction monitoring (SRM): A process by which the ion
current of a product ion of a specific m/z value produced from a
precursor of a specified m/z value is monitored. This process is used
to gain specificity for analytes in complex matrices.
Spectral skewing: A term used to describe the phenomenon of
changes in relative intensities of mass spectral peaks between different
spectra during an acquisition of GC/MS data due to the changes in
concentration of the analyte in the ion source as the chromatographic
component elutes. This phenomenon is not observed in ion trap
(quadrupole or magnetic) or time-of-flight (TOF) mass spectrometers.
The TOF-MS records all ions sent down the flight tube in a single
430 Appendix B

pulse. The ion trap mass spectrometer records all the ions that have
been stored in the trap.
Tandem mass spectrometry: See MS/MS.
Time-of-flight (TOF) analyzer: A device that measures the flight time of
ions having a given kinetic energy through a fixed distance. The flight times
of ions are proportional to m/z values.
torr (Torr): See pascal.
Total ion current (TIC): The sum of all the separate ion currents con­
tributed by the ions that make up the spectrum.
Unified atomic mass unit (u): See dalton.
Unimolecular ion decomposition: Refers to the fact that the decom­
position of an ion under EI conditions is due solely to the ion’s internal
energy. The pressure in the ion source is sufficiently low so as to prevent
bimolecular or other collision reactions (the collision of an ion resulting in
either a fragmentation or an increase in internal energy that will result in
fragmentation).