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Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of
ion An ion () is an atom or molecule with a net electrical charge. The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by conve ...
s. The results are presented as a ''
mass spectrum A mass spectrum is a histogram plot of intensity vs. ''mass-to-charge ratio'' (''m/z'') in a chemical sample, usually acquired using an instrument called a ''mass spectrometer''. Not all mass spectra of a given substance are the same; for example ...
'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or
isotopic signature An isotopic signature (also isotopic fingerprint) is a ratio of non-radiogenic ' stable isotopes', stable radiogenic isotopes, or unstable radioactive isotopes of particular elements in an investigated material. The ratios of isotopes in a sample ...
of a sample, the masses of particles and of
molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...
s, and to elucidate the chemical identity or structure of molecules and other
chemical compound A chemical compound is a chemical substance composed of many identical molecules (or molecular entities) containing atoms from more than one chemical element held together by chemical bonds. A molecule consisting of atoms of only one element ...
s. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is
ionized Ionization, or Ionisation is the process by which an atom or a molecule acquires a negative or positive charge by gaining or losing electrons, often in conjunction with other chemical changes. The resulting electrically charged atom or molecule ...
, for example by bombarding it with a beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragments) are then separated according to their mass-to-charge ratio, for example by accelerating them and subjecting them to an electric or magnetic field: ions of the same mass-to-charge ratio will undergo the same amount of deflection. The ions are detected by a mechanism capable of detecting charged particles, such as an
electron multiplier An electron multiplier is a vacuum-tube structure that multiplies incident charges. In a process called secondary emission, a single electron can, when bombarded on secondary-emissive material, induce emission of roughly 1 to 3 electrons. If an el ...
. Results are displayed as spectra of the signal intensity of detected ions as a function of the mass-to-charge ratio. The atoms or molecules in the sample can be identified by correlating known masses (e.g. an entire molecule) to the identified masses or through a characteristic fragmentation pattern.


History of the mass spectrometer

In 1886, Eugen Goldstein observed rays in
gas discharge Electric discharge in gases occurs when electric current flows through a gaseous medium due to ionization of the gas. Depending on several factors, the discharge may radiate visible light. The properties of electric discharges in gases are studied ...
s under low pressure that traveled away from the
anode An anode is an electrode of a polarized electrical device through which conventional current enters the device. This contrasts with a cathode, an electrode of the device through which conventional current leaves the device. A common mnemonic ...
and through channels in a perforated
cathode A cathode is the electrode from which a conventional current leaves a polarized electrical device. This definition can be recalled by using the mnemonic ''CCD'' for ''Cathode Current Departs''. A conventional current describes the direction in wh ...
, opposite to the direction of negatively charged
cathode rays Cathode rays or electron beam (e-beam) are streams of electrons observed in discharge tubes. If an evacuated glass tube is equipped with two electrodes and a voltage is applied, glass behind the positive electrode is observed to glow, due to el ...
(which travel from cathode to anode). Goldstein called these positively charged anode rays "Kanalstrahlen"; the standard translation of this term into English is "
canal rays An anode ray (also positive ray or canal ray) is a beam of positive ions that is created by certain types of gas-discharge tubes. They were first observed in Crookes tubes during experiments by the German scientist Eugen Goldstein, in 1886. La ...
".
Wilhelm Wien Wilhelm Carl Werner Otto Fritz Franz Wien (; 13 January 1864 – 30 August 1928) was a German physicist who, in 1893, used theories about heat and electromagnetism to deduce Wien's displacement law, which calculates the emission of a blackbody ...
found that strong electric or magnetic fields deflected the canal rays and, in 1899, constructed a device with perpendicular electric and magnetic fields that separated the positive rays according to their charge-to-mass ratio (''Q/m''). Wien found that the charge-to-mass ratio depended on the nature of the gas in the discharge tube. English scientist
J. J. Thomson Sir Joseph John Thomson (18 December 1856 – 30 August 1940) was a British physicist and Nobel Laureate in Physics, credited with the discovery of the electron, the first subatomic particle to be discovered. In 1897, Thomson showed that ...
later improved on the work of Wien by reducing the pressure to create the mass spectrograph. The word ''spectrograph'' had become part of the international scientific vocabulary by 1884. Early ''spectrometry'' devices that measured the mass-to-charge ratio of ions were called '' mass spectrographs'' which consisted of instruments that recorded a
spectrum A spectrum (plural ''spectra'' or ''spectrums'') is a condition that is not limited to a specific set of values but can vary, without gaps, across a continuum. The word was first used scientifically in optics to describe the rainbow of colors ...
of mass values on a photographic plate. A ''mass spectroscope'' is similar to a ''mass spectrograph'' except that the beam of ions is directed onto a phosphor screen. A mass spectroscope configuration was used in early instruments when it was desired that the effects of adjustments be quickly observed. Once the instrument was properly adjusted, a photographic plate was inserted and exposed. The term mass spectroscope continued to be used even though the direct illumination of a phosphor screen was replaced by indirect measurements with an oscilloscope. The use of the term ''mass spectroscopy'' is now discouraged due to the possibility of confusion with light spectroscopy. Mass spectrometry is often abbreviated as ''mass-spec'' or simply as ''MS''. Modern techniques of mass spectrometry were devised by
Arthur Jeffrey Dempster Arthur Jeffrey Dempster (August 14, 1886 – March 11, 1950) was a Canadian-American physicist best known for his work in mass spectrometry and his discovery in 1935 of the uranium isotope 235U. Early life and education Dempster was born i ...
and F.W. Aston in 1918 and 1919 respectively.
Sector mass spectrometer A sector instrument is a general term for a class of mass spectrometer that uses a static electric (E) or magnetic (B) sector or some combination of the two (separately in space) as a mass analyzer. Popular combinations of these sectors have been ...
s known as
calutron A calutron is a mass spectrometer originally designed and used for separating the isotopes of uranium. It was developed by Ernest Lawrence during the Manhattan Project and was based on his earlier invention, the cyclotron. Its name was derive ...
s were developed by Ernest O. Lawrence and used for separating the
isotopes of uranium Uranium (92U) is a naturally occurring radioactive element that has no stable isotope. It has two primordial isotopes, uranium-238 and uranium-235, that have long half-lives and are found in appreciable quantity in the Earth's crust. The d ...
during the
Manhattan Project The Manhattan Project was a research and development undertaking during World War II that produced the first nuclear weapons. It was led by the United States with the support of the United Kingdom and Canada. From 1942 to 1946, the project w ...
. Calutron mass spectrometers were used for
uranium enrichment Enriched uranium is a type of uranium in which the percent composition of uranium-235 (written 235U) has been increased through the process of isotope separation. Naturally occurring uranium is composed of three major isotopes: uranium-238 (238 ...
at the Oak Ridge, Tennessee Y-12 plant established during World War II. In 1989, half of the
Nobel Prize in Physics ) , image = Nobel Prize.png , alt = A golden medallion with an embossed image of a bearded man facing left in profile. To the left of the man is the text "ALFR•" then "NOBEL", and on the right, the text (smaller) "NAT•" then " ...
was awarded to
Hans Dehmelt Hans Georg Dehmelt (; 9 September 1922 – 7 March 2017) was a German and American physicist, who was awarded a Nobel Prize in Physics in 1989, for co-developing the ion trap technique ( Penning trap) with Wolfgang Paul, for which they shared one ...
and Wolfgang Paul for the development of the ion trap technique in the 1950s and 1960s. In 2002, the
Nobel Prize in Chemistry ) , image = Nobel Prize.png , alt = A golden medallion with an embossed image of a bearded man facing left in profile. To the left of the man is the text "ALFR•" then "NOBEL", and on the right, the text (smaller) "NAT•" then "M ...
was awarded to
John Bennett Fenn John Bennett Fenn (June 15, 1917December 10, 2010) was an American professor of analytical chemistry who was awarded a share of the Nobel Prize in Chemistry in 2002. Fenn shared half of the award with Koichi Tanaka for their work in mass spectro ...
for the development of
electrospray ionization Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules becaus ...
(ESI) and
Koichi Tanaka is a Japanese electrical engineer who shared the Nobel Prize in Chemistry in 2002 for developing a novel method for mass spectrometric analyses of biological macromolecules with John Bennett Fenn and Kurt Wüthrich (the latter for work in N ...
for the development of soft laser desorption (SLD) and their application to the ionization of biological macromolecules, especially proteins.


Parts of a mass spectrometer

A mass spectrometer consists of three components: an ion source, a mass analyzer, and a detector. The '' ionizer'' converts a portion of the sample into ions. There is a wide variety of ionization techniques, depending on the phase (solid, liquid, gas) of the sample and the efficiency of various ionization mechanisms for the unknown species. An extraction system removes ions from the sample, which are then targeted through the mass analyzer and into the ''detector''. The differences in masses of the fragments allows the mass analyzer to sort the ions by their mass-to-charge ratio. The detector measures the value of an indicator quantity and thus provides data for calculating the abundances of each ion present. Some detectors also give spatial information, e.g., a multichannel plate.


Theoretical example

The following describes the operation of a spectrometer mass analyzer, which is of the
sector Sector may refer to: Places * Sector, West Virginia, U.S. Geometry * Circular sector, the portion of a disc enclosed by two radii and a circular arc * Hyperbolic sector, a region enclosed by two radii and a hyperbolic arc * Spherical sector, a p ...
type. (Other analyzer types are treated below.) Consider a sample of sodium chloride (table salt). In the ion source, the sample is
vapor In physics, a vapor (American English) or vapour (British English and Canadian English; see spelling differences) is a substance in the gas phase at a temperature lower than its critical temperature,R. H. Petrucci, W. S. Harwood, and F. G. Her ...
ized (turned into
gas Gas is one of the four fundamental states of matter (the others being solid, liquid, and plasma). A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or ...
) and ionized (transformed into electrically charged particles) into
sodium Sodium is a chemical element with the symbol Na (from Latin ''natrium'') and atomic number 11. It is a soft, silvery-white, highly reactive metal. Sodium is an alkali metal, being in group 1 of the periodic table. Its only stable ...
(Na+) and
chloride The chloride ion is the anion (negatively charged ion) Cl−. It is formed when the element chlorine (a halogen) gains an electron or when a compound such as hydrogen chloride is dissolved in water or other polar solvents. Chloride sa ...
(Cl) ions. Sodium atoms and ions are monoisotopic, with a mass of about 23 u. Chloride atoms and ions come in two stable
isotopes Isotopes are two or more types of atoms that have the same atomic number (number of protons in their nuclei) and position in the periodic table (and hence belong to the same chemical element), and that differ in nucleon numbers (mass numbers) ...
with masses of approximately 35 u (at a natural abundance of about 75 percent) and approximately 37 u (at a natural abundance of about 25 percent). The analyzer part of the spectrometer contains
electric Electricity is the set of physical phenomena associated with the presence and motion of matter that has a property of electric charge. Electricity is related to magnetism, both being part of the phenomenon of electromagnetism, as described by ...
and magnetic fields, which exert forces on ions traveling through these fields. The speed of a charged particle may be increased or decreased while passing through the electric field, and its direction may be altered by the magnetic field. The magnitude of the deflection of the moving ion's trajectory depends on its mass-to-charge ratio. Lighter ions get deflected by the magnetic force more than heavier ions (based on Newton's second law of motion, ''F'' = ''ma''). The streams of sorted ions pass from the analyzer to the detector, which records the relative abundance of each ion type. This information is used to determine the chemical element composition of the original sample (i.e. that both sodium and chlorine are present in the sample) and the isotopic composition of its constituents (the ratio of 35Cl to 37Cl).


Creating ions

The
ion source An ion source is a device that creates atomic and molecular ions. Ion sources are used to form ions for mass spectrometers, optical emission spectrometers, particle accelerators, ion implanters and ion engines. Electron ionization Electron ...
is the part of the mass spectrometer that ionizes the material under analysis (the analyte). The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for
gas Gas is one of the four fundamental states of matter (the others being solid, liquid, and plasma). A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or ...
es and
vapor In physics, a vapor (American English) or vapour (British English and Canadian English; see spelling differences) is a substance in the gas phase at a temperature lower than its critical temperature,R. H. Petrucci, W. S. Harwood, and F. G. Her ...
s. In chemical ionization sources, the analyte is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and
solid Solid is one of the four fundamental states of matter (the others being liquid, gas, and plasma). The molecules in a solid are closely packed together and contain the least amount of kinetic energy. A solid is characterized by structural ...
biological samples include
electrospray ionization Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules becaus ...
(invented by John Fenn) and
matrix-assisted laser desorption/ionization In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of ...
(MALDI, initially developed as a similar technique "Soft Laser Desorption (SLD)" by K. Tanaka for which a Nobel Prize was awarded and as MALDI by M. Karas and F. Hillenkamp).


Hard ionization and soft ionization

In mass spectrometry, ionization refers to the production of gas phase ions suitable for resolution in the mass analyser or mass filter. Ionization occurs in the
ion source An ion source is a device that creates atomic and molecular ions. Ion sources are used to form ions for mass spectrometers, optical emission spectrometers, particle accelerators, ion implanters and ion engines. Electron ionization Electron ...
. There are several
ion source An ion source is a device that creates atomic and molecular ions. Ion sources are used to form ions for mass spectrometers, optical emission spectrometers, particle accelerators, ion implanters and ion engines. Electron ionization Electron ...
s available; each has advantages and disadvantages for particular applications. For example, electron ionization (EI) gives a high degree of fragmentation, yielding highly detailed mass spectra which when skilfully analysed can provide important information for structural elucidation/characterisation and facilitate identification of unknown compounds by comparison to mass spectral libraries obtained under identical operating conditions. However, EI is not suitable for coupling to HPLC, i.e. LC-MS, since at atmospheric pressure, the filaments used to generate electrons burn out rapidly. Thus EI is coupled predominantly with GC, i.e. GC-MS, where the entire system is under high vacuum. Hard ionization techniques are processes which impart high quantities of residual energy in the subject molecule invoking large degrees of fragmentation (i.e. the systematic rupturing of bonds acts to remove the excess energy, restoring stability to the resulting ion). Resultant ions tend to have ''m/z'' lower than the molecular ion (other than in the case of proton transfer and not including isotope peaks). The most common example of hard ionization is electron ionization (EI). Soft ionization refers to the processes which impart little residual energy onto the subject molecule and as such result in little fragmentation. Examples include
fast atom bombardment Fast atom bombardment (FAB) is an ionization technique used in mass spectrometry in which a beam of high energy atoms strikes a surface to create ions. It was developed by Michael Barber at the University of Manchester in 1980. When a beam of hig ...
(FAB), chemical ionization (CI),
atmospheric-pressure chemical ionization Atmospheric pressure chemical ionization (APCI) is an ionization method used in mass spectrometry which utilizes gas-phase ion-molecule reactions at atmospheric pressure (105 Pa), commonly coupled with high-performance liquid chromatography (HPLC ...
(APCI), atmospheric-pressure photoionization (APPI),
electrospray ionization Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules becaus ...
(ESI),
desorption electrospray ionization Desorption electrospray ionization (DESI) is an ambient ionization technique that can be coupled to mass spectrometry (MS) for chemical analysis of samples at atmospheric conditions. Coupled ionization sources-MS systems are popular in chemical a ...
(DESI), and
matrix-assisted laser desorption/ionization In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of ...
(MALDI).


Inductively coupled plasma

Inductively coupled plasma An inductively coupled plasma (ICP) or transformer coupled plasma (TCP) is a type of plasma source in which the energy is supplied by electric currents which are produced by electromagnetic induction, that is, by time-varying magnetic fields. Ope ...
(ICP) sources are used primarily for cation analysis of a wide array of sample types. In this source, a plasma that is electrically neutral overall, but that has had a substantial fraction of its atoms ionized by high temperature, is used to atomize introduced sample molecules and to further strip the outer electrons from those atoms. The plasma is usually generated from argon gas, since the first ionization energy of argon atoms is higher than the first of any other elements except He, F and Ne, but lower than the second ionization energy of all except the most electropositive metals. The heating is achieved by a radio-frequency current passed through a coil surrounding the plasma.


Photoionization mass spectrometry

Photoionization Photoionization is the physical process in which an ion is formed from the interaction of a photon with an atom or molecule. Cross section Not every interaction between a photon and an atom, or molecule, will result in photoionization. The prob ...
can be used in experiments which seek to use mass spectrometry as a means of resolving chemical kinetics mechanisms and isomeric product branching. In such instances a high energy photon, either X-ray or uv, is used to dissociate stable gaseous molecules in a carrier gas of He or Ar. In instances where a synchrotron light source is utilized, a tuneable photon energy can be utilized to acquire a photoionization efficiency curve which can be used in conjunction with the charge ratio m/z to fingerprint molecular and ionic species. More recently
atmospheric pressure photoionization Atmospheric pressure photoionization (APPI) is a soft ionization method used in mass spectrometry (MS) usually coupled to liquid chromatography (LC). Molecules are ionized using a vacuum ultraviolet (VUV) light source operating at atmospheric pre ...
(APPI) has been developed to ionize molecules mostly as effluents of LC-MS systems.


Ambient ionization

Some applications for
ambient ionization Ambient ionization is a form of ionization in which ions are formed in an ion source outside the mass spectrometer without sample preparation or separation. Ions can be formed by extraction into charged electrospray droplets, thermally desorbed a ...
include environmental applications as well as clinical applications. In these techniques, ions form in an ion source outside the mass spectrometer. Sampling becomes easy as the samples don't need previous separation nor preparation. Some examples of ambient ionization techniques are
DESI DESI may refer to * Desorption electrospray ionization * Drug Efficacy Study Implementation Drug Efficacy Study Implementation (DESI) was a program begun by the Food and Drug Administration (FDA) in the 1960s after the requirement (in the Kefauve ...
, SESI, LAESI, desorption atmospheric-pressure chemical ionization (DAPCI), and desorption atmospheric pressure photoionization
DAPPI Desorption atmospheric pressure photoionization (DAPPI) is an ambient ionization technique for mass spectrometry that uses hot solvent vapor for desorption in conjunction with photoionization. Ambient Ionization techniques allow for direct analysis ...
among others.


Other ionization techniques

Others include
glow discharge A glow discharge is a plasma formed by the passage of electric current through a gas. It is often created by applying a voltage between two electrodes in a glass tube containing a low-pressure gas. When the voltage exceeds a value called the st ...
,
field desorption Field desorption (FD) is a method of ion formation used in mass spectrometry (MS) in which a high-potential electric field is applied to an ''emitter'' with a sharp surface, such as a razor blade, or more commonly, a filament from which tiny "whis ...
(FD),
fast atom bombardment Fast atom bombardment (FAB) is an ionization technique used in mass spectrometry in which a beam of high energy atoms strikes a surface to create ions. It was developed by Michael Barber at the University of Manchester in 1980. When a beam of hig ...
(FAB), thermospray, desorption/ionization on silicon (DIOS), Direct Analysis in Real Time (DART),
atmospheric pressure chemical ionization Atmospheric pressure chemical ionization (APCI) is an ionization method used in mass spectrometry which utilizes gas-phase ion-molecule reactions at atmospheric pressure (105 Pa), commonly coupled with high-performance liquid chromatography (HPLC ...
(APCI),
secondary ion mass spectrometry Secondary-ion mass spectrometry (SIMS) is a technique used to analyze the composition of solid surfaces and thin films by sputtering the surface of the specimen with a focused primary ion beam and collecting and analyzing ejected secondary ions. ...
(SIMS), spark ionization and
thermal ionization Thermal ionization, also known as surface ionization or contact ionization, is a physical process whereby the atoms are desorbed from a hot surface, and in the process are ionized. Thermal ionization is used to make simple ion sources, for mass ...
(TIMS).


Mass selection

Mass analyzers separate the ions according to their mass-to-charge ratio. The following two laws govern the dynamics of charged particles in electric and magnetic fields in vacuum: :\mathbf = Q (\mathbf + \mathbf \times \mathbf) ( Lorentz force law); :\mathbf=m\mathbf (
Newton's second law Newton's laws of motion are three basic laws of classical mechanics that describe the relationship between the motion of an object and the forces acting on it. These laws can be paraphrased as follows: # A body remains at rest, or in moti ...
of motion in the non-relativistic case, i.e. valid only at ion velocity much lower than the speed of light). Here F is the force applied to the ion, ''m'' is the mass of the ion, a is the acceleration, ''Q'' is the ion charge, E is the electric field, and v × B is the
vector cross product In mathematics, the cross product or vector product (occasionally directed area product, to emphasize its geometric significance) is a binary operation on two vectors in a three-dimensional oriented Euclidean vector space (named here E), and is d ...
of the ion velocity and the magnetic field Equating the above expressions for the force applied to the ion yields: : (m/Q)\mathbf = \mathbf+ \mathbf \times \mathbf. This
differential equation In mathematics, a differential equation is an equation that relates one or more unknown functions and their derivatives. In applications, the functions generally represent physical quantities, the derivatives represent their rates of change, an ...
is the classic equation of motion for
charged particle In physics, a charged particle is a particle with an electric charge. It may be an ion, such as a molecule or atom with a surplus or deficit of electrons relative to protons. It can also be an electron or a proton, or another elementary pa ...
s. Together with the particle's initial conditions, it completely determines the particle's motion in space and time in terms of ''m/Q''. Thus mass spectrometers could be thought of as "mass-to-charge spectrometers". When presenting data, it is common to use the (officially)
dimensionless A dimensionless quantity (also known as a bare quantity, pure quantity, or scalar quantity as well as quantity of dimension one) is a quantity to which no physical dimension is assigned, with a corresponding SI unit of measurement of one (or 1) ...
''m/z'', where z is the number of elementary charges (''e'') on the ion (z=Q/e). This quantity, although it is informally called the mass-to-charge ratio, more accurately speaking represents the ratio of the mass number and the charge number, ''z''. There are many types of mass analyzers, using either static or dynamic fields, and magnetic or electric fields, but all operate according to the above differential equation. Each analyzer type has its strengths and weaknesses. Many mass spectrometers use two or more mass analyzers for tandem mass spectrometry (MS/MS). In addition to the more common mass analyzers listed below, there are others designed for special situations. There are several important analyzer characteristics. The mass resolving power is the measure of the ability to distinguish two peaks of slightly different ''m/z''. The mass accuracy is the ratio of the ''m/z'' measurement error to the true m/z. Mass accuracy is usually measured in ppm or
milli mass unit The milli mass unit or (mmu) is used as a unit of mass by some scientific authors even though this unit is not defined by the IUPAP red book nor by the IUPAC green book. It is a short form of the more formally correct "milli unified atomic mass u ...
s. The mass range is the range of ''m/z'' amenable to analysis by a given analyzer. The linear dynamic range is the range over which ion signal is linear with analyte concentration. Speed refers to the time frame of the experiment and ultimately is used to determine the number of spectra per unit time that can be generated.


Sector instruments

A sector field mass analyzer uses a static electric and/or magnetic field to affect the path and/or
velocity Velocity is the directional speed of an object in motion as an indication of its rate of change in position as observed from a particular frame of reference and as measured by a particular standard of time (e.g. northbound). Velocity i ...
of the charged particles in some way. As shown above, sector instruments bend the trajectories of the ions as they pass through the mass analyzer, according to their mass-to-charge ratios, deflecting the more charged and faster-moving, lighter ions more. The analyzer can be used to select a narrow range of ''m/z'' or to scan through a range of ''m/z'' to catalog the ions present.


Time-of-flight

The
time-of-flight Time of flight (ToF) is the measurement of the time taken by an object, particle or wave (be it acoustic, electromagnetic, etc.) to travel a distance through a medium. This information can then be used to measure velocity or path length, or as a w ...
(TOF) analyzer uses an electric field to accelerate the ions through the same
potential Potential generally refers to a currently unrealized ability. The term is used in a wide variety of fields, from physics to the social sciences to indicate things that are in a state where they are able to change in ways ranging from the simple r ...
, and then measures the time they take to reach the detector. If the particles all have the same
charge Charge or charged may refer to: Arts, entertainment, and media Films * '' Charge, Zero Emissions/Maximum Speed'', a 2011 documentary Music * ''Charge'' (David Ford album) * ''Charge'' (Machel Montano album) * ''Charge!!'', an album by The Aqu ...
, their kinetic energies will be identical, and their
velocities Velocity is the directional speed of an object in motion as an indication of its rate of change in position as observed from a particular frame of reference and as measured by a particular standard of time (e.g. northbound). Velocity is a ...
will depend only on their
mass Mass is an intrinsic property of a body. It was traditionally believed to be related to the quantity of matter in a physical body, until the discovery of the atom and particle physics. It was found that different atoms and different eleme ...
es. Ions with a lower mass will reach the detector first. However, in reality, even particles with the same m/z can arrive at different times at the detector, because they have different initial velocities. The initial velocity is often not dependent on the mass of the ion, and will turn into a difference in the final velocity. Because of this, ions with the same m/z ratio will reach the detector at a variety of times, which broadens the peaks shown on the count vs m/z plot, but will generally not change the central location of the peaks, since the starting velocity of ions is generally centered at zero. To fix this problem, time-lag focusing/ delayed extraction has been coupled with TOF-MS.


Quadrupole mass filter

Quadrupole mass analyzer The quadrupole mass analyzer, originally conceived by Nobel Laureate Wolfgang Paul and his student Helmut Steinwedel, also known as quadrupole mass filter, is one type of mass analyzer used in mass spectrometry. As the name implies, it consists o ...
s use oscillating electrical fields to selectively stabilize or destabilize the paths of ions passing through a
radio frequency Radio frequency (RF) is the oscillation rate of an alternating electric current or voltage or of a magnetic, electric or electromagnetic field or mechanical system in the frequency range from around to around . This is roughly between the ...
(RF)
quadrupole A quadrupole or quadrapole is one of a sequence of configurations of things like electric charge or current, or gravitational mass that can exist in ideal form, but it is usually just part of a multipole expansion of a more complex structure refl ...
field created between four parallel rods. Only the ions in a certain range of mass/charge ratio are passed through the system at any time, but changes to the potentials on the rods allow a wide range of m/z values to be swept rapidly, either continuously or in a succession of discrete hops. A quadrupole mass analyzer acts as a mass-selective filter and is closely related to the quadrupole ion trap, particularly the linear quadrupole ion trap except that it is designed to pass the untrapped ions rather than collect the trapped ones, and is for that reason referred to as a transmission quadrupole. A magnetically enhanced quadrupole mass analyzer includes the addition of a magnetic field, either applied axially or transversely. This novel type of instrument leads to an additional performance enhancement in terms of resolution and/or sensitivity depending upon the magnitude and orientation of the applied magnetic field. A common variation of the transmission quadrupole is the triple quadrupole mass spectrometer. The “triple quad” has three consecutive quadrupole stages, the first acting as a mass filter to transmit a particular incoming ion to the second quadrupole, a collision chamber, wherein that ion can be broken into fragments. The third quadrupole also acts as a mass filter, to transmit a particular fragment ion to the detector. If a quadrupole is made to rapidly and repetitively cycle through a range of mass filter settings, full spectra can be reported. Likewise, a triple quad can be made to perform various scan types characteristic of
tandem mass spectrometry Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A com ...
.


Ion traps


Three-dimensional quadrupole ion trap

The quadrupole ion trap works on the same physical principles as the quadrupole mass analyzer, but the ions are trapped and sequentially ejected. Ions are trapped in a mainly quadrupole RF field, in a space defined by a ring electrode (usually connected to the main RF potential) between two endcap electrodes (typically connected to DC or auxiliary AC potentials). The sample is ionized either internally (e.g. with an electron or laser beam), or externally, in which case the ions are often introduced through an aperture in an endcap electrode. There are many mass/charge separation and isolation methods but the most commonly used is the mass instability mode in which the RF potential is ramped so that the orbit of ions with a mass are stable while ions with mass ''b'' become unstable and are ejected on the ''z''-axis onto a detector. There are also non-destructive analysis methods. Ions may also be ejected by the resonance excitation method, whereby a supplemental oscillatory excitation voltage is applied to the endcap electrodes, and the trapping voltage amplitude and/or excitation voltage frequency is varied to bring ions into a resonance condition in order of their mass/charge ratio.


Cylindrical ion trap

The cylindrical ion trap mass spectrometer (CIT) is a derivative of the quadrupole ion trap where the electrodes are formed from flat rings rather than hyperbolic shaped electrodes. The architecture lends itself well to miniaturization because as the size of a trap is reduced, the shape of the electric field near the center of the trap, the region where the ions are trapped, forms a shape similar to that of a hyperbolic trap.


Linear quadrupole ion trap

A
linear quadrupole ion trap A quadrupole ion trap or paul trap is a type of ion trap that uses dynamic electric fields to trap charged particles. They are also called radio frequency (RF) traps or Paul traps in honor of Wolfgang Paul, who invented the device and shared the ...
is similar to a quadrupole ion trap, but it traps ions in a two dimensional quadrupole field, instead of a three-dimensional quadrupole field as in a 3D quadrupole ion trap. Thermo Fisher's LTQ ("linear trap quadrupole") is an example of the linear ion trap. A toroidal ion trap can be visualized as a linear quadrupole curved around and connected at the ends or as a cross-section of a 3D ion trap rotated on edge to form the toroid, donut-shaped trap. The trap can store large volumes of ions by distributing them throughout the ring-like trap structure. This toroidal shaped trap is a configuration that allows the increased miniaturization of an ion trap mass analyzer. Additionally, all ions are stored in the same trapping field and ejected together simplifying detection that can be complicated with array configurations due to variations in detector alignment and machining of the arrays. As with the toroidal trap, linear traps and 3D quadrupole ion traps are the most commonly miniaturized mass analyzers due to their high sensitivity, tolerance for mTorr pressure, and capabilities for single analyzer tandem mass spectrometry (e.g. product ion scans).


Orbitrap

Orbitrap In mass spectrometry, Orbitrap is 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. The image current from the trapped ions is ...
instruments are similar to
Fourier-transform ion cyclotron resonance Fourier-transform ion cyclotron resonance mass spectrometry is a type of mass analyzer (or mass spectrometer) for determining the mass-to-charge ratio (''m''/''z'') of ions based on the cyclotron frequency of the ions in a fixed magnetic field. T ...
mass spectrometers (see text below). Ions are
electrostatic Electrostatics is a branch of physics that studies electric charges at rest ( static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amb ...
ally trapped in an orbit around a central, spindle shaped electrode. The electrode confines the ions so that they both orbit around the central electrode and oscillate back and forth along the central electrode's long axis. This oscillation generates an image current in the detector plates which is recorded by the instrument. The frequencies of these image currents depend on the mass-to-charge ratios of the ions. Mass spectra are obtained by
Fourier transformation A Fourier transform (FT) is a mathematical transform that decomposes functions into frequency components, which are represented by the output of the transform as a function of frequency. Most commonly functions of time or space are transformed ...
of the recorded image currents. Orbitraps have a high mass accuracy, high sensitivity and a good dynamic range.


Fourier-transform ion cyclotron resonance

Fourier-transform mass spectrometry (FTMS), or more precisely
Fourier-transform ion cyclotron resonance Fourier-transform ion cyclotron resonance mass spectrometry is a type of mass analyzer (or mass spectrometer) for determining the mass-to-charge ratio (''m''/''z'') of ions based on the cyclotron frequency of the ions in a fixed magnetic field. T ...
MS, measures mass by detecting the image current produced by ions
cyclotron A cyclotron is a type of particle accelerator invented by Ernest O. Lawrence in 1929–1930 at the University of California, Berkeley, and patented in 1932. Lawrence, Ernest O. ''Method and apparatus for the acceleration of ions'', filed: Jan ...
ing in the presence of a magnetic field. Instead of measuring the deflection of ions with a detector such as an
electron multiplier An electron multiplier is a vacuum-tube structure that multiplies incident charges. In a process called secondary emission, a single electron can, when bombarded on secondary-emissive material, induce emission of roughly 1 to 3 electrons. If an el ...
, the ions are injected into a Penning trap (a static electric/magnetic
ion trap An ion trap is a combination of electric and/or magnetic fields used to capture charged particles — known as ions — often in a system isolated from an external environment. Atomic and molecular ion traps have a number of applications in phy ...
) where they effectively form part of a circuit. Detectors at fixed positions in space measure the electrical signal of ions which pass near them over time, producing a periodic signal. Since the frequency of an ion's cycling is determined by its mass-to-charge ratio, this can be deconvoluted by performing a Fourier transform on the signal.
FTMS Fourier-transform ion cyclotron resonance mass spectrometry is a type of mass analyzer (or mass spectrometer) for determining the mass-to-charge ratio (''m''/''z'') of ions based on the cyclotron frequency of the ions in a fixed magnetic field. T ...
has the advantage of high sensitivity (since each ion is "counted" more than once) and much higher resolution and thus precision.
Ion cyclotron resonance Ion cyclotron resonance is a phenomenon related to the movement of ions in a magnetic field. It is used for accelerating ions in a cyclotron, and for measuring the masses of an ionized analyte in mass spectrometry, particularly with Fourier transfo ...
(ICR) is an older mass analysis technique similar to FTMS except that ions are detected with a traditional detector. Ions trapped in a Penning trap are excited by an RF electric field until they impact the wall of the trap, where the detector is located. Ions of different mass are resolved according to impact time.


Detectors

The final element of the mass spectrometer is the detector. The detector records either the charge induced or the current produced when an ion passes by or hits a surface. In a scanning instrument, the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what ''m/Q'') will produce a
mass spectrum A mass spectrum is a histogram plot of intensity vs. ''mass-to-charge ratio'' (''m/z'') in a chemical sample, usually acquired using an instrument called a ''mass spectrometer''. Not all mass spectra of a given substance are the same; for example ...
, a record of ions as a function of ''m/Q''. Typically, some type of
electron multiplier An electron multiplier is a vacuum-tube structure that multiplies incident charges. In a process called secondary emission, a single electron can, when bombarded on secondary-emissive material, induce emission of roughly 1 to 3 electrons. If an el ...
is used, though other detectors including
Faraday cup A Faraday cup is a metal (conductive) cup designed to catch charged particles in vacuum. The resulting current can be measured and used to determine the number of ions or electrons hitting the cup. The Faraday cup was named after Michael Fara ...
s and ion-to-photon detectors are also used. Because the number of ions leaving the mass analyzer at a particular instant is typically quite small, considerable amplification is often necessary to get a signal. Microchannel plate detectors are commonly used in modern commercial instruments. In
FTMS Fourier-transform ion cyclotron resonance mass spectrometry is a type of mass analyzer (or mass spectrometer) for determining the mass-to-charge ratio (''m''/''z'') of ions based on the cyclotron frequency of the ions in a fixed magnetic field. T ...
and
Orbitrap In mass spectrometry, Orbitrap is 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. The image current from the trapped ions is ...
s, the detector consists of a pair of metal surfaces within the mass analyzer/ion trap region which the ions only pass near as they oscillate. No direct current is produced, only a weak AC image current is produced in a circuit between the electrodes. Other inductive detectors have also been used.


Tandem mass spectrometry

A tandem mass spectrometer is one capable of multiple rounds of mass spectrometry, usually separated by some form of molecule fragmentation. For example, one mass analyzer can isolate one
peptide Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. ...
from many entering a mass spectrometer. A second mass analyzer then stabilizes the peptide ions while they collide with a gas, causing them to fragment by
collision-induced dissociation Collision-induced dissociation (CID), also known as collisionally activated dissociation (CAD), is a mass spectrometry technique to induce fragmentation of selected ions in the gas phase. The selected ions (typically molecular ions or protonate ...
(CID). A third mass analyzer then sorts the fragments produced from the peptides. Tandem MS can also be done in a single mass analyzer over time, as in a quadrupole ion trap. There are various methods for fragmenting molecules for tandem MS, including
collision-induced dissociation Collision-induced dissociation (CID), also known as collisionally activated dissociation (CAD), is a mass spectrometry technique to induce fragmentation of selected ions in the gas phase. The selected ions (typically molecular ions or protonate ...
(CID),
electron capture dissociation Electron-capture dissociation (ECD) is a method of fragmenting gas-phase ions for structure elucidation of peptides and proteins in tandem mass spectrometry. It is one of the most widely used techniques for activation and dissociation of mass sel ...
(ECD),
electron transfer dissociation Electron-transfer dissociation (ETD) is a method of fragmenting multiply-charged gaseous macromolecules in a mass spectrometer between the stages of tandem mass spectrometry (MS/MS). Similar to electron-capture dissociation, ETD induces fragmenta ...
(ETD), infrared multiphoton dissociation (IRMPD),
blackbody infrared radiative dissociation Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A com ...
(BIRD),
electron-detachment dissociation Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A comm ...
(EDD) and surface-induced dissociation (SID). An important application using tandem mass spectrometry is in protein identification. Tandem mass spectrometry enables a variety of experimental sequences. Many commercial mass spectrometers are designed to expedite the execution of such routine sequences as selected reaction monitoring (SRM) and precursor ion scanning. In SRM, the first analyzer allows only a single mass through and the second analyzer monitors for multiple user-defined fragment ions. SRM is most often used with scanning instruments where the second mass analysis event is duty cycle limited. These experiments are used to increase specificity of detection of known molecules, notably in pharmacokinetic studies. Precursor ion scanning refers to monitoring for a specific loss from the precursor ion. The first and second mass analyzers scan across the spectrum as partitioned by a user-defined ''m/z'' value. This experiment is used to detect specific motifs within unknown molecules. Another type of tandem mass spectrometry used for radiocarbon dating is
accelerator mass spectrometry Accelerator mass spectrometry (AMS) is a form of mass spectrometry that accelerates ions to extraordinarily high kinetic energies before mass analysis. The special strength of AMS among the mass spectrometric methods is its power to separate a r ...
(AMS), which uses very high voltages, usually in the mega-volt range, to accelerate negative ions into a type of tandem mass spectrometer. The METLIN Metabolite and Chemical Entity Database is the largest repository of experimental
tandem mass spectrometry Tandem mass spectrometry, also known as MS/MS or MS2, is a technique in instrumental analysis where two or more mass analyzers are coupled together using an additional reaction step to increase their abilities to analyse chemical samples. A com ...
data acquired from standards. The tandem mass spectrometry data on over 850,000 molecular standards (as of 24 August 2020) is provided to facilitate the identification of chemical entities from tandem mass spectrometry experiments. In addition to the identification of known molecules it is also useful for identifying unknowns using its similarity searching/analysis. All tandem mass spectrometry data comes from the experimental analysis of standards at multiple collision energies and in both positive and negative ionization modes.


Common mass spectrometer configurations and techniques

When a specific combination of source, analyzer, and detector becomes conventional in practice, a compound
acronym An acronym is a word or name formed from the initial components of a longer name or phrase. Acronyms are usually formed from the initial letters of words, as in ''NATO'' (''North Atlantic Treaty Organization''), but sometimes use syllables, as ...
may arise to designate it succinctly. One example is
MALDI-TOF In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of ...
, which refers to a combination of a
matrix-assisted laser desorption/ionization In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of ...
source with a
time-of-flight Time of flight (ToF) is the measurement of the time taken by an object, particle or wave (be it acoustic, electromagnetic, etc.) to travel a distance through a medium. This information can then be used to measure velocity or path length, or as a w ...
mass analyzer. Other examples include inductively coupled plasma-mass spectrometry (ICP-MS), accelerator mass spectrometry (AMS), thermal ionization-mass spectrometry (TIMS) and spark source mass spectrometry (SSMS). Certain applications of mass spectrometry have developed monikers that although strictly speaking would seem to refer to a broad application, in practice have come instead to connote a specific or a limited number of instrument configurations. An example of this is
isotope-ratio mass spectrometry Isotope-ratio mass spectrometry (IRMS) is a specialization of mass spectrometry, in which mass spectrometric methods are used to measure the relative abundance of isotopes in a given sample. This technique has two different applications in the ea ...
(IRMS), which refers in practice to the use of a limited number of sector based mass analyzers; this name is used to refer to both the application and the instrument used for the application.


Separation techniques combined with mass spectrometry

An important enhancement to the mass resolving and mass determining capabilities of mass spectrometry is using it in tandem with chromatographic and other separation techniques.


Gas chromatography

A common combination is
gas Gas is one of the four fundamental states of matter (the others being solid, liquid, and plasma). A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or ...
chromatography-mass spectrometry (GC/MS or GC-MS). In this technique, a
gas chromatograph Gas chromatography (GC) is a common type of chromatography used in analytical chemistry for separating and analyzing compounds that can be vaporized without decomposition. Typical uses of GC include testing the purity of a particular substance, ...
is used to separate different compounds. This stream of separated compounds is fed online into the
ion An ion () is an atom or molecule with a net electrical charge. The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by conve ...
source, a
metal A metal (from Greek μέταλλον ''métallon'', "mine, quarry, metal") is a material that, when freshly prepared, polished, or fractured, shows a lustrous appearance, and conducts electricity and heat relatively well. Metals are typicall ...
lic filament to which
voltage Voltage, also known as electric pressure, electric tension, or (electric) potential difference, is the difference in electric potential between two points. In a static electric field, it corresponds to the work needed per unit of charge to ...
is applied. This filament emits electrons which ionize the compounds. The ions can then further fragment, yielding predictable patterns. Intact ions and fragments pass into the mass spectrometer's analyzer and are eventually detected. However, the high temperatures (300°C) used in the GC-MS injection port (and oven) can result in thermal degradation of injected molecules, thus resulting in the measurement of degradation products instead of the actual molecule(s) of interest.


Liquid chromatography

Similarly to gas chromatography MS (GC-MS), liquid chromatography-mass spectrometry (LC/MS or LC-MS) separates compounds chromatographically before they are introduced to the ion source and mass spectrometer. It differs from GC-MS in that the mobile phase is liquid, usually a mixture of
water Water (chemical formula ) is an Inorganic compound, inorganic, transparent, tasteless, odorless, and Color of water, nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living ...
and organic
solvent A solvent (s) (from the Latin '' solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for ...
s, instead of gas. Most commonly, an
electrospray ionization Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules becaus ...
source is used in LC-MS. Other popular and commercially available LC-MS ion sources are
atmospheric pressure chemical ionization Atmospheric pressure chemical ionization (APCI) is an ionization method used in mass spectrometry which utilizes gas-phase ion-molecule reactions at atmospheric pressure (105 Pa), commonly coupled with high-performance liquid chromatography (HPLC ...
and
atmospheric pressure photoionization Atmospheric pressure photoionization (APPI) is a soft ionization method used in mass spectrometry (MS) usually coupled to liquid chromatography (LC). Molecules are ionized using a vacuum ultraviolet (VUV) light source operating at atmospheric pre ...
. There are also some newly developed ionization techniques like laser spray.


Capillary electrophoresis–mass spectrometry

Capillary electrophoresis–mass spectrometry (CE-MS) is a technique that combines the liquid separation process of
capillary electrophoresis Capillary electrophoresis (CE) is a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels. Very often, CE refers to capillary zone electrophoresis (CZE), but other elect ...
with mass spectrometry. CE-MS is typically coupled to electrospray ionization.


Ion mobility

Ion mobility spectrometry-mass spectrometry (IMS/MS or IMMS) is a technique where ions are first separated by drift time through some neutral gas under an applied electrical potential gradient before being introduced into a mass spectrometer. Drift time is a measure of the radius relative to the charge of the ion. The duty cycle of IMS (the time over which the experiment takes place) is longer than most mass spectrometric techniques, such that the mass spectrometer can sample along the course of the IMS separation. This produces data about the IMS separation and the mass-to-charge ratio of the ions in a manner similar to LC-MS. The duty cycle of IMS is short relative to liquid chromatography or gas chromatography separations and can thus be coupled to such techniques, producing triple modalities such as LC/IMS/MS.


Data and analysis


Data representations

Mass spectrometry produces various types of data. The most common data representation is the
mass spectrum A mass spectrum is a histogram plot of intensity vs. ''mass-to-charge ratio'' (''m/z'') in a chemical sample, usually acquired using an instrument called a ''mass spectrometer''. Not all mass spectra of a given substance are the same; for example ...
. Certain types of mass spectrometry data are best represented as a mass chromatogram. Types of chromatograms include selected ion monitoring (SIM), total ion current (TIC), and selected reaction monitoring (SRM), among many others. Other types of mass spectrometry data are well represented as a three-dimensional contour map. In this form, the mass-to-charge, ''m/z'' is on the ''x''-axis, intensity the ''y''-axis, and an additional experimental parameter, such as time, is recorded on the ''z''-axis.


Data analysis

Mass spectrometry data analysis is specific to the type of experiment producing the data. General subdivisions of data are fundamental to understanding any data. Many mass spectrometers work in either ''negative ion mode'' or ''positive ion mode''. It is very important to know whether the observed ions are negatively or positively charged. This is often important in determining the neutral mass but it also indicates something about the nature of the molecules. Different types of ion source result in different arrays of fragments produced from the original molecules. An electron ionization source produces many fragments and mostly single-charged (1-) radicals (odd number of electrons), whereas an electrospray source usually produces non-radical quasimolecular ions that are frequently multiply charged. Tandem mass spectrometry purposely produces fragment ions post-source and can drastically change the sort of data achieved by an experiment. Knowledge of the origin of a sample can provide insight into the component molecules of the sample and their fragmentations. A sample from a synthesis/manufacturing process will probably contain impurities chemically related to the target component. A crudely prepared biological sample will probably contain a certain amount of salt, which may form
adduct An adduct (from the Latin ''adductus'', "drawn toward" alternatively, a contraction of "addition product") is a product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all co ...
s with the analyte molecules in certain analyses. Results can also depend heavily on sample preparation and how it was run/introduced. An important example is the issue of which matrix is used for MALDI spotting, since much of the energetics of the desorption/ionization event is controlled by the matrix rather than the laser power. Sometimes samples are spiked with sodium or another ion-carrying species to produce adducts rather than a protonated species. Mass spectrometry can measure molar mass, molecular structure, and sample purity. Each of these questions requires a different experimental procedure; therefore, adequate definition of the experimental goal is a prerequisite for collecting the proper data and successfully interpreting it.


Interpretation of mass spectra

Since the precise structure or
peptide sequence Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A ...
of a molecule is deciphered through the set of fragment masses, the interpretation of
mass spectra A mass spectrum is a histogram plot of intensity vs. ''mass-to-charge ratio'' (''m/z'') in a chemical sample, usually acquired using an instrument called a ''mass spectrometer''. Not all mass spectra of a given substance are the same; for example ...
requires combined use of various techniques. Usually the first strategy for identifying an unknown compound is to compare its experimental mass spectrum against a library of mass spectra. If no matches result from the search, then manual interpretation or software assisted interpretation of mass spectra must be performed. Computer simulation of
ionization Ionization, or Ionisation is the process by which an atom or a molecule acquires a negative or positive charge by gaining or losing electrons, often in conjunction with other chemical changes. The resulting electrically charged atom or molecul ...
and fragmentation processes occurring in mass spectrometer is the primary tool for assigning structure or peptide sequence to a molecule. An ''
a priori ("from the earlier") and ("from the later") are Latin phrases used in philosophy to distinguish types of knowledge, justification, or argument by their reliance on empirical evidence or experience. knowledge is independent from current ...
'' structural information is fragmented '' in silico'' and the resulting pattern is compared with observed spectrum. Such simulation is often supported by a fragmentation library that contains published patterns of known decomposition reactions.
Software Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work. ...
taking advantage of this idea has been developed for both small molecules and proteins. Analysis of mass spectra can also be spectra with accurate mass. A mass-to-charge ratio value (''m/z'') with only integer precision can represent an immense number of theoretically possible ion structures; however, more precise mass figures significantly reduce the number of candidate molecular formulas. A computer algorithm called formula generator calculates all molecular formulas that theoretically fit a given
mass Mass is an intrinsic property of a body. It was traditionally believed to be related to the quantity of matter in a physical body, until the discovery of the atom and particle physics. It was found that different atoms and different eleme ...
with specified tolerance. A recent technique for structure elucidation in mass spectrometry, called precursor ion fingerprinting, identifies individual pieces of structural information by conducting a search of the tandem spectra of the molecule under investigation against a library of the product-ion spectra of structurally characterized precursor ions.


Applications

Mass spectrometry has both qualitative and quantitative uses. These include identifying unknown compounds, determining the isotopic composition of elements in a molecule, and determining the structure of a compound by observing its fragmentation. Other uses include quantifying the amount of a compound in a sample or studying the fundamentals of
gas phase ion chemistry Gas phase ion chemistry is a field of science encompassed within both chemistry and physics. It is the science that studies ions and molecules in the gas phase, most often enabled by some form of mass spectrometry. By far the most important appl ...
(the chemistry of ions and neutrals in a vacuum). MS is now commonly used in analytical laboratories that study physical, chemical, or biological properties of a great variety of compounds. Quantitation can be relative (analyzed relative to a reference sample) or absolute (analyzed using a standard curve method). As an analytical technique it possesses distinct advantages such as: Increased sensitivity over most other analytical techniques because the analyzer, as a mass-charge filter, reduces background interference, Excellent specificity from characteristic fragmentation patterns to identify unknowns or confirm the presence of suspected compounds, Information about molecular weight, Information about the isotopic abundance of elements, Temporally resolved chemical data. A few of the disadvantages of the method is that it often fails to distinguish between optical and geometrical isomers and the positions of substituent in o-, m- and p- positions in an aromatic ring. Also, its scope is limited in identifying hydrocarbons that produce similar fragmented ions.


Isotope ratio MS: isotope dating and tracing

Mass spectrometry is also used to determine the isotopic composition of elements within a sample. Differences in mass among isotopes of an element are very small, and the less abundant isotopes of an element are typically very rare, so a very sensitive instrument is required. These instruments, sometimes referred to as isotope ratio mass spectrometers (IR-MS), usually use a single magnet to bend a beam of ionized particles towards a series of
Faraday cup A Faraday cup is a metal (conductive) cup designed to catch charged particles in vacuum. The resulting current can be measured and used to determine the number of ions or electrons hitting the cup. The Faraday cup was named after Michael Fara ...
s which convert particle impacts to electric current. A fast on-line analysis of
deuterium Deuterium (or hydrogen-2, symbol or deuterium, also known as heavy hydrogen) is one of two stable isotopes of hydrogen (the other being protium, or hydrogen-1). The nucleus of a deuterium atom, called a deuteron, contains one proton and one ...
content of water can be done using flowing afterglow mass spectrometry, FA-MS. Probably the most sensitive and accurate mass spectrometer for this purpose is the accelerator mass spectrometer (AMS). This is because it provides ultimate sensitivity, capable of measuring individual atoms and measuring nuclides with a dynamic range of ~1015 relative to the major stable isotope. Isotope ratios are important markers of a variety of processes. Some isotope ratios are used to determine the age of materials for example as in carbon dating. Labeling with stable isotopes is also used for protein quantification. (see protein characterization below)


Membrane-introduction mass spectrometry: measuring gases in solution

Membrane-introduction mass spectrometry combines the isotope ratio MS with a reaction chamber/cell separated by a gas-permeable membrane. This method allows the study of gases as they evolve in solution. This method has been extensively used for the study of the production of oxygen by Photosystem II.


Trace gas analysis

Several techniques use ions created in a dedicated ion source injected into a flow tube or a drift tube: selected ion flow tube (SIFT-MS), and proton transfer reaction (PTR-MS), are variants of chemical ionization dedicated for trace gas analysis of air, breath or liquid headspace using well defined reaction time allowing calculations of analyte concentrations from the known reaction kinetics without the need for internal standard or calibration. Another technique with applications in trace gas analysis field is
secondary electrospray ionization Secondary electro-spray ionization (SESI) is an ambient ionization technique for the analysis of trace concentrations of vapors, where a nano-electrospray produces charging agents that collide with the analyte molecules directly in gas-phase. In t ...
(SESI-MS), which is a variant of
electrospray ionization Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules becaus ...
. SESI consist of an electrospray plume of pure acidified solvent that interacts with neutral vapors.  Vapor molecules get ionized at atmospheric pressure when charge is transferred from the ions formed in the electrospray to the molecules. One advantage of this approach is that it is compatible with most ESI-MS systems.


Atom probe

An atom probe is an instrument that combines
time-of-flight Time of flight (ToF) is the measurement of the time taken by an object, particle or wave (be it acoustic, electromagnetic, etc.) to travel a distance through a medium. This information can then be used to measure velocity or path length, or as a w ...
mass spectrometry and field-evaporation microscopy to map the location of individual atoms.


Pharmacokinetics

Pharmacokinetics is often studied using mass spectrometry because of the complex nature of the matrix (often blood or urine) and the need for high sensitivity to observe low dose and long time point data. The most common instrumentation used in this application is LC-MS with a
triple quadrupole mass spectrometer A triple quadrupole mass spectrometer (TQMS), is a tandem mass spectrometer consisting of two quadrupole mass analyzers in series, with a (non-mass-resolving) radio frequency (RF)–only quadrupole between them to act as a cell for collision-in ...
. Tandem mass spectrometry is usually employed for added specificity. Standard curves and internal standards are used for quantitation of usually a single pharmaceutical in the samples. The samples represent different time points as a pharmaceutical is administered and then metabolized or cleared from the body. Blank or t=0 samples taken before administration are important in determining background and ensuring data integrity with such complex sample matrices. Much attention is paid to the linearity of the standard curve; however it is not uncommon to use
curve fitting Curve fitting is the process of constructing a curve, or mathematical function, that has the best fit to a series of data points, possibly subject to constraints. Curve fitting can involve either interpolation, where an exact fit to the data i ...
with more complex functions such as quadratics since the response of most mass spectrometers is less than linear across large concentration ranges. There is currently considerable interest in the use of very high sensitivity mass spectrometry for microdosing studies, which are seen as a promising alternative to
animal experimentation Animal testing, also known as animal experimentation, animal research, and ''in vivo'' testing, is the use of non-human animals in experiments that seek to control the variables that affect the behavior or biological system under study. This ...
. Recent studies show that
secondary electrospray ionization Secondary electro-spray ionization (SESI) is an ambient ionization technique for the analysis of trace concentrations of vapors, where a nano-electrospray produces charging agents that collide with the analyte molecules directly in gas-phase. In t ...
(SESI) is a powerful technique to monitor drug kinetics via breath analysis. Because breath is naturally produced, several datapoints can be readily collected. This allows for the number of collected data-points to be greatly increased. In animal studies, this approach SESI can reduce animal sacrifice. In humans, SESI-MS non-invasive analysis of breath can help study the kinetics of drugs at a personalized level.


Protein characterization

Mass spectrometry is an important method for the characterization and sequencing of proteins. The two primary methods for ionization of whole proteins are
electrospray ionization Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules becaus ...
(ESI) and
matrix-assisted laser desorption/ionization In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of ...
(MALDI). In keeping with the performance and mass range of available mass spectrometers, two approaches are used for characterizing proteins. In the first, intact proteins are ionized by either of the two techniques described above, and then introduced to a mass analyzer. This approach is referred to as " top-down" strategy of protein analysis. The top-down approach however is largely limited to low-throughput single-protein studies. In the second, proteins are enzymatically digested into smaller peptides using
protease A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the ...
s such as
trypsin Trypsin is an enzyme in the first section of the small intestine that starts the digestion of protein molecules by cutting these long chains of amino acids into smaller pieces. It is a serine protease from the PA clan superfamily, found in the d ...
or
pepsin Pepsin is an endopeptidase that breaks down proteins into smaller peptides. It is produced in the gastric chief cells of the stomach lining and is one of the main digestive enzymes in the digestive systems of humans and many other animals, w ...
, either in solution or in gel after electrophoretic separation. Other proteolytic agents are also used. The collection of peptide products are often separated by chromatography prior to introduction to the mass analyzer. When the characteristic pattern of peptides is used for the identification of the protein the method is called peptide mass fingerprinting (PMF), if the identification is performed using the sequence data determined in tandem MS analysis it is called
de novo peptide sequencing In mass spectrometry, de novo peptide sequencing is the method in which a peptide amino acid sequence is determined from tandem mass spectrometry. Knowing the amino acid sequence of peptides from a protein digest is essential for studying the biolo ...
. These procedures of protein analysis are also referred to as the " bottom-up" approach, and have also been used to analyse the distribution and position of post-translational modifications such as phosphorylation on proteins. A third approach is also beginning to be used, this intermediate "middle-down" approach involves analyzing proteolytic peptides that are larger than the typical tryptic peptide.


Space exploration

As a standard method for analysis, mass spectrometers have reached other planets and moons. Two were taken to
Mars Mars is the fourth planet from the Sun and the second-smallest planet in the Solar System, only being larger than Mercury. In the English language, Mars is named for the Roman god of war. Mars is a terrestrial planet with a thin at ...
by the
Viking program The ''Viking'' program consisted of a pair of identical American space probes, ''Viking 1'' and ''Viking 2'', which landed on Mars in 1976. Each spacecraft was composed of two main parts: an orbiter designed to photograph the surface of Mars f ...
. In early 2005 the Cassini–Huygens mission delivered a specialized GC-MS instrument aboard the Huygens probe through the atmosphere of Titan, the largest moon of the planet Saturn. This instrument analyzed atmospheric samples along its descent trajectory and was able to vaporize and analyze samples of Titan's frozen, hydrocarbon covered surface once the probe had landed. These measurements compare the abundance of isotope(s) of each particle comparatively to earth's natural abundance. Also on board the Cassini–Huygens spacecraft was an ion and neutral mass spectrometer which had been taking measurements of Titan's atmospheric composition as well as the composition of
Enceladus Enceladus is the sixth-largest moon of Saturn (19th largest in the Solar System). It is about in diameter, about a tenth of that of Saturn's largest moon, Titan. Enceladus is mostly covered by fresh, clean ice, making it one of the most refle ...
' plumes. A
Thermal and Evolved Gas Analyzer The Thermal and Evolved Gas Analyzer (TEGA) is a scientific instrument aboard the ''Phoenix'' spacecraft, a Mars lander which landed and operated on the planet Mars in 2008. TEGA's design is based on experience gained from the failed Mars Polar ...
mass spectrometer was carried by the Mars Phoenix Lander launched in 2007. Mass spectrometers are also widely used in space missions to measure the composition of plasmas. For example, the Cassini spacecraft carried the Cassini Plasma Spectrometer (CAPS), which measured the mass of ions in Saturn's magnetosphere.


Respired gas monitor

Mass spectrometers were used in hospitals for respiratory gas analysis beginning around 1975 through the end of the century. Some are probably still in use but none are currently being manufactured. Found mostly in the operating room, they were a part of a complex system, in which respired gas samples from patients undergoing anesthesia were drawn into the instrument through a valve mechanism designed to sequentially connect up to 32 rooms to the mass spectrometer. A computer directed all operations of the system. The data collected from the mass spectrometer was delivered to the individual rooms for the anesthesiologist to use. The uniqueness of this magnetic sector mass spectrometer may have been the fact that a plane of detectors, each purposely positioned to collect all of the ion species expected to be in the samples, allowed the instrument to simultaneously report all of the gases respired by the patient. Although the mass range was limited to slightly over 120 u, fragmentation of some of the heavier molecules negated the need for a higher detection limit.


Preparative mass spectrometry

The primary function of mass spectrometry is as a tool for chemical analyses based on detection and quantification of ions according to their mass-to-charge ratio. However, mass spectrometry also shows promise for material synthesis. Ion soft landing is characterized by deposition of intact species on surfaces at low kinetic energies which precludes the fragmentation of the incident species. The soft landing technique was first reported in 1977 for the reaction of low energy sulfur containing ions on a lead surface.


See also

* Dumas method of molecular weight determination * Evolved gas analysis *
Helium mass spectrometer A helium mass spectrometer is an instrument commonly used to detect and locate small leaks. It was initially developed in the Manhattan Project during World War II to find extremely small leaks in the gas diffusion process of uranium enrichment pl ...
*
Isotope dilution Isotope dilution analysis is a method of determining the quantity of chemical substances. In its most simple conception, the method of isotope dilution comprises the addition of known amounts of isotopically enriched substance to the analyzed samp ...
* MassBank (database), a Japanese spectral database * Mass spectrometry imaging *
Mass spectrometry software Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry. Proteomics software In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS2) experiments are used f ...
* Micro-arrays for mass spectrometry * Nanoscale secondary ion mass spectrometry *
Reflectron A reflectron (mass reflectron) is a type of time-of-flight mass spectrometer (TOF MS) that comprises a pulsed ion source, field-free region, ion mirror, and ion detector and uses a static or time dependent electric field in the ion mirror to rev ...


References


Bibliography

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External links

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Interactive tutorial on mass spectra
National High Magnetic Field Laboratory

An interactive application simulating the console of a mass spectrometer
Realtime Mass Spectra simulation
Tool to simulate mass spectra in the browser {{DEFAULTSORT:Mass Spectrometry Chemical pathology Spectrometers Measuring instruments Scientific instruments Scientific techniques Clinical pathology