Mass spectrometry

Mass spectrometry

Overview
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio
Mass-to-charge ratio
The mass-to-charge ratio ratio is a physical quantity that is widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of lithography, electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger...

 of charged particles.
It is used for determining masses of particles, for determining the elemental composition of a sample or molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

, and for elucidating the chemical structures of molecules, such as peptide
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...

s and other chemical compound
Chemical compound
A chemical compound is a pure chemical substance consisting of two or more different chemical elements that can be separated into simpler substances by chemical reactions. Chemical compounds have a unique and defined chemical structure; they consist of a fixed ratio of atoms that are held together...

s. The MS principle consists of ionizing chemical compounds to generate charged molecules or molecule fragments and measuring their mass-to-charge ratio
Mass-to-charge ratio
The mass-to-charge ratio ratio is a physical quantity that is widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of lithography, electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger...

s.
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Encyclopedia
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio
Mass-to-charge ratio
The mass-to-charge ratio ratio is a physical quantity that is widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of lithography, electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger...

 of charged particles.
It is used for determining masses of particles, for determining the elemental composition of a sample or molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

, and for elucidating the chemical structures of molecules, such as peptide
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...

s and other chemical compound
Chemical compound
A chemical compound is a pure chemical substance consisting of two or more different chemical elements that can be separated into simpler substances by chemical reactions. Chemical compounds have a unique and defined chemical structure; they consist of a fixed ratio of atoms that are held together...

s. The MS principle consists of ionizing chemical compounds to generate charged molecules or molecule fragments and measuring their mass-to-charge ratio
Mass-to-charge ratio
The mass-to-charge ratio ratio is a physical quantity that is widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of lithography, electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger...

s. In a typical MS procedure:
  1. A sample is loaded onto the MS instrument, and undergoes vaporization
    Vaporization
    Vaporization of an element or compound is a phase transition from the liquid or solid phase to gas phase. There are three types of vaporization: evaporation, boiling and sublimation....

  2. The components of the sample are ionized by one of a variety of methods (e.g., by impacting them with an electron beam), which results in the formation of charged particles (ion
    Ion
    An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

    s)
  3. The ions are separated according to their mass-to-charge ratio
    Mass-to-charge ratio
    The mass-to-charge ratio ratio is a physical quantity that is widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of lithography, electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger...

     in an analyzer by electromagnetic
    Electromagnetism
    Electromagnetism is one of the four fundamental interactions in nature. The other three are the strong interaction, the weak interaction and gravitation...

     fields
  4. The ions are detected, usually by a quantitative method
  5. The ion signal is processed into mass spectra


MS instruments consist of three modules:
  • An ion source
    Ion source
    An ion source is an electro-magnetic device that is used to create charged particles. These are used primarily to form ions for mass spectrometers, optical emission spectrometers, particle accelerators, ion implanters and ion engines.- Electron ionization :...

    , which can convert gas phase sample molecules into ions (or, in the case of electrospray ionization, move ions that exist in solution into the gas phase)
  • A mass analyzer, which sorts the ions by their masses by applying electromagnetic fields
  • A detector, which measures the value of an indicator quantity and thus provides data for calculating the abundances of each ion present

The technique has both qualitative
Qualitative research
Qualitative research is a method of inquiry employed in many different academic disciplines, traditionally in the social sciences, but also in market research and further contexts. Qualitative researchers aim to gather an in-depth understanding of human behavior and the reasons that govern such...

 and quantitative
Quantitative analysis (chemistry)
In chemistry, quantitative analysis is the determination of the absolute or relative abundance of one, several or all particular substance present in a sample....

 uses. These include identifying unknown compounds, determining the isotopic
Isotope
Isotopes are variants of atoms of a particular chemical element, which have differing numbers of neutrons. Atoms of a particular element by definition must contain the same number of protons but may have a distinct number of neutrons which differs from atom to atom, without changing the designation...

 composition of elements in a molecule, and determining the structure
Structure
Structure is a fundamental, tangible or intangible notion referring to the recognition, observation, nature, and permanence of patterns and relationships of entities. This notion may itself be an object, such as a built structure, or an attribute, such as the structure of society...

 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
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 applications for this science is in studying the...

 (the chemistry of ions and neutrals in a vacuum). MS is now in very common use in analytical laboratories that study physical, chemical, or biological properties of a great variety of compounds.

Etymology


The word spectrograph had become part of the international scientific vocabulary
International Scientific Vocabulary
International scientific vocabulary comprises scientific and specialized words whose language of origin may or may not be certain, but which are in current use in several modern languages. The name "International Scientific Vocabulary" was first used by Philip Gove in Webster’s Third New...

 by 1884.
The linguistic roots
Root (linguistics)
The root word is the primary lexical unit of a word, and of a word family , which carries the most significant aspects of semantic content and cannot be reduced into smaller constituents....

 are a combination and removal of bound morpheme
Bound morpheme
In morphology, a bound morpheme is a morpheme that only appears as part of a larger word; a free morpheme is one that can stand alone.Affixes are always bound. English language affixes are either prefixes or suffixes. E.g., -ment in "shipment" and pre- in "prefix"...

s and free morphemes which relate to the terms spectr-um and phot-ograph-ic plate. Early spectrometry devices that measured the mass-to-charge ratio of ions were called mass spectrographs
Spectrograph
A spectrograph is an instrument that separates an incoming wave into a frequency spectrum. There are several kinds of machines referred to as spectrographs, depending on the precise nature of the waves...

 which consisted of instruments that recorded a spectrum
Spectrum
A spectrum is a condition that is not limited to a specific set of values but can vary infinitely within a continuum. The word saw its first scientific use within the field of optics to describe the rainbow of colors in visible light when separated using a prism; it has since been applied by...

 of mass values on a photographic plate
Photographic plate
Photographic plates preceded photographic film as a means of photography. A light-sensitive emulsion of silver salts was applied to a glass plate. This form of photographic material largely faded from the consumer market in the early years of the 20th century, as more convenient and less fragile...

. A mass spectroscope is similar to a mass spectrograph except that the beam of ions is directed onto a phosphor
Phosphor
A phosphor, most generally, is a substance that exhibits the phenomenon of luminescence. Somewhat confusingly, this includes both phosphorescent materials, which show a slow decay in brightness , and fluorescent materials, where the emission decay takes place over tens of nanoseconds...

 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
Oscilloscope
An oscilloscope is a type of electronic test instrument that allows observation of constantly varying signal voltages, usually as a two-dimensional graph of one or more electrical potential differences using the vertical or 'Y' axis, plotted as a function of time,...

. The use of the term mass spectroscopy is now discouraged due to the possibility of confusion with light spectroscopy
Spectroscopy
Spectroscopy is the study of the interaction between matter and radiated energy. Historically, spectroscopy originated through the study of visible light dispersed according to its wavelength, e.g., by a prism. Later the concept was expanded greatly to comprise any interaction with radiative...

. Mass spectrometry is often abbreviated as mass-spec or simply as MS.

History


In 1886, Eugen Goldstein
Eugen Goldstein
Eugen Goldstein was a German physicist. He was an early investigator of discharge tubes, the discoverer of anode rays, and is sometimes credited with the discovery of the proton.- Life :...

 observed rays in gas discharges under low pressure that traveled away from the anode and through channels in a perforated cathode
Cathode
A cathode is an electrode through which electric current flows out of a polarized electrical device. Mnemonic: CCD .Cathode polarity is not always negative...

, opposite to the direction of negatively charged cathode rays (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". Wilhelm Wien
Wilhelm Wien
Wilhelm Carl Werner Otto Fritz Franz Wien 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 at any temperature from the emission at any one reference temperature.He also formulated an...

 found that strong electric or magnetic fields deflected the canal rays and, in 1899, constructed a device with parallel 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 later improved on the work of Wien by reducing the pressure to create a mass spectrograph.

The first application of mass spectrometry to the analysis of amino acids and peptides was reported in 1958. Carl-Ove Andersson highlighted the main fragment ions observed in the ionization of methyl esters.

Some of the modern techniques of mass spectrometry were devised by Arthur Jeffrey Dempster
Arthur Jeffrey Dempster
Arthur Jeffrey Dempster was a Canadian-American physicist best known for his work in mass spectrometry and his discovery of the uranium isotope 235U.-Biography:...

 and F.W. Aston in 1918 and 1919 respectively. In 1989, half of the Nobel Prize in Physics
Nobel Prize in Physics
The Nobel Prize in Physics is awarded once a year by the Royal Swedish Academy of Sciences. It is one of the five Nobel Prizes established by the will of Alfred Nobel in 1895 and awarded since 1901; the others are the Nobel Prize in Chemistry, Nobel Prize in Literature, Nobel Peace Prize, and...

 was awarded to Hans Dehmelt and Wolfgang Paul
Wolfgang Paul
Wolfgang Paul was a German physicist, who co-developed the non-magnetic quadrupole mass filter which laid the foundation for what we now call an ion trap...

 for the development of the ion trap technique in the 1950s and 1960s. In 2002, the Nobel Prize in Chemistry
Nobel Prize in Chemistry
The Nobel Prize in Chemistry is awarded annually by the Royal Swedish Academy of Sciences to scientists in the various fields of chemistry. It is one of the five Nobel Prizes established by the will of Alfred Nobel in 1895, awarded for outstanding contributions in chemistry, physics, literature,...

 was awarded to John Bennett Fenn for the development of electrospray ionization
Electrospray ionization
Electrospray ionization is a technique used in mass spectrometry to produce ions. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized...

 (ESI) and Koichi Tanaka
Koichi Tanaka
is a Japanese scientist 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 Wuthrich ....

 for the development of soft laser desorption
Soft laser desorption
Soft laser desorption is laser desorption of large molecules that results in ionization without fragmentation. "Soft" in the context of ion formation means forming ions without breaking chemical bonds...

 (SLD) and their application to the ionization of biological macromolecules, especially proteins.

Simplified example



The following example describes the operation of a spectrometer mass analyzer, which is of the sector
Sector instrument
A sector instrument is a general term for a class of mass spectrometer that uses a static electric or magnetic sector or some combination of the two as a mass analyzer. A popular combination of these sectors has been the BEB...

 type. (Other analyzer types are treated below.) Consider a sample of sodium chloride
Sodium chloride
Sodium chloride, also known as salt, common salt, table salt or halite, is an inorganic compound with the formula NaCl. Sodium chloride is the salt most responsible for the salinity of the ocean and of the extracellular fluid of many multicellular organisms...

 (table salt). In the ion source, the sample is vapor
Vapor
A vapor or vapour is a substance in the gas phase at a temperature lower than its critical point....

ized (turned into gas
Gas
Gas is one of the three classical states of matter . Near absolute zero, a substance exists as a solid. As heat is added to this substance it melts into a liquid at its melting point , boils into a gas at its boiling point, and if heated high enough would enter a plasma state in which the electrons...

) and ionized (transformed into electrically charged particles) into sodium
Sodium
Sodium is a chemical element with the symbol Na and atomic number 11. It is a soft, silvery-white, highly reactive metal and is a member of the alkali metals; its only stable isotope is 23Na. It is an abundant element that exists in numerous minerals, most commonly as sodium chloride...

 (Na+) and chloride
Chloride
The chloride ion is formed when the element chlorine, a halogen, picks up one electron to form an anion Cl−. The salts of hydrochloric acid HCl contain chloride ions and can also be called chlorides. The chloride ion, and its salts such as sodium chloride, are very soluble in water...

 (Cl-) ions. Sodium atoms and ions are monoisotopic
Isotope
Isotopes are variants of atoms of a particular chemical element, which have differing numbers of neutrons. Atoms of a particular element by definition must contain the same number of protons but may have a distinct number of neutrons which differs from atom to atom, without changing the designation...

, with a mass of about 23 amu. Chloride atoms and ions come in two isotopes with masses of approximately 35 amu (at a natural abundance of about 75 percent) and approximately 37 amu (at a natural abundance of about 25 percent). The analyzer part of the spectrometer contains electric
Electric field
In physics, an electric field surrounds electrically charged particles and time-varying magnetic fields. The electric field depicts the force exerted on other electrically charged objects by the electrically charged particle the field is surrounding...

 and magnetic
Magnetic field
A magnetic field is a mathematical description of the magnetic influence of electric currents and magnetic materials. The magnetic field at any given point is specified by both a direction and a magnitude ; as such it is a vector field.Technically, a magnetic field is a pseudo vector;...

 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
Newton's laws of motion
Newton's laws of motion are three physical laws that form the basis for classical mechanics. They describe the relationship between the forces acting on a body and its motion due to those forces...

, 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 is the part of the mass spectrometer that ionizes the material under analysis (the analyte). The ions are then transported by magnetic
Magnetic field
A magnetic field is a mathematical description of the magnetic influence of electric currents and magnetic materials. The magnetic field at any given point is specified by both a direction and a magnitude ; as such it is a vector field.Technically, a magnetic field is a pseudo vector;...

 or electric field
Electric field
In physics, an electric field surrounds electrically charged particles and time-varying magnetic fields. The electric field depicts the force exerted on other electrically charged objects by the electrically charged particle the field is surrounding...

s to the mass analyzer.

Techniques for ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

ization have been key to determining what types of samples can be analyzed by mass spectrometry.
Electron ionization
Electron ionization
Electron ionization is an ionization method in which energetic electrons interact with gas phase atoms or molecules to produce ions...

 and chemical ionization
Chemical ionization
Chemical ionization is an ionization technique used in mass spectrometry. Chemical ionization is a lower energy process than electron ionization. The lower energy yields less fragmentation, and usually a simpler spectrum...

 are used for gas
Gas
Gas is one of the three classical states of matter . Near absolute zero, a substance exists as a solid. As heat is added to this substance it melts into a liquid at its melting point , boils into a gas at its boiling point, and if heated high enough would enter a plasma state in which the electrons...

es and vapor
Vapor
A vapor or vapour is a substance in the gas phase at a temperature lower than its critical point....

s. In chemical ionization
Chemical ionization
Chemical ionization is an ionization technique used in mass spectrometry. Chemical ionization is a lower energy process than electron ionization. The lower energy yields less fragmentation, and usually a simpler spectrum...

 sources, the analyte is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid
Liquid
Liquid is one of the three classical states of matter . Like a gas, a liquid is able to flow and take the shape of a container. Some liquids resist compression, while others can be compressed. Unlike a gas, a liquid does not disperse to fill every space of a container, and maintains a fairly...

 and solid
Solid
Solid is one of the three classical states of matter . It is characterized by structural rigidity and resistance to changes of shape or volume. Unlike a liquid, a solid object does not flow to take on the shape of its container, nor does it expand to fill the entire volume available to it like a...

 biological samples include electrospray ionization
Electrospray ionization
Electrospray ionization is a technique used in mass spectrometry to produce ions. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized...

 (invented by John Fenn) and matrix-assisted laser desorption/ionization
Matrix-assisted laser desorption/ionization
Matrix-assisted laser desorption/ionization is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules and large organic molecules , which tend to be fragile and fragment when ionized by more conventional ionization methods...

 (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).

Inductively coupled plasma


Inductively coupled plasma
ICP-MS
Inductively coupled plasma mass spectrometry is a type of mass spectrometry that is highly sensitive and capable of the determination of a range of metals and several non-metals at concentrations below one part in 1012...

 (ICP) sources are used primarily for cation analysis of a wide array of sample types. In this type of Ion Source Technology, a 'flame' of 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, O, 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.

Other ionization techniques


Others include glow discharge, field desorption
Field desorption
Field desorption /field ionization refers to an ion source for mass spectrometry first reported by Beckey in 1969. In field ionization, 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 "whiskers"...

 (FD), fast atom bombardment
Fast atom bombardment
Fast atom bombardment is an ionization technique used in mass spectrometry. The material to be analyzed is mixed with a non-volatile chemical protection environment called a matrix and is bombarded under vacuum with a high energy beam of atoms. The atoms are typically from an inert gas such as...

 (FAB), thermospray
Thermospray
Thermospray is a form of atmospheric pressure ionization in mass spectrometry. It transfers ions from the liquid phase to the gas phase for analysis. It is particularly useful in liquid chromatography-mass spectrometry....

, desorption/ionization on silicon (DIOS), Direct Analysis in Real Time (DART)
DART ion source
DART is an atmospheric pressure ion source that instantaneously ionizes gases, liquids and solids in open air under ambient conditions. It was developed in 2005 by Laramee and Cody and is now marketed commercially by JEOL and IonSense...

, atmospheric pressure chemical ionization
Atmospheric pressure chemical ionization
Atmospheric-pressure chemical ionization is an ionization method used in mass spectrometry. It is a form of chemical ionization which takes place at atmospheric pressure.-How it works:...

 (APCI), secondary ion mass spectrometry
Secondary ion mass spectrometry
Secondary ion mass spectrometry is a technique used in materials science and surface science 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
Spark ionization
Spark ionization is a method used to produce gas phase ions from a solid sample. The prepared solid sample is vaporized and partially ionized by an intermittent discharge or spark. This technique is primarily used in the field of mass spectrometry...

 and thermal ionization
Thermal ionization
In thermal ionization, also referred to as surface ionization, chemically-purified material loaded onto a filament which is then heated to cause some of the material to be ionized as it boils off the hot filament...

 (TIMS).
Ion attachment ionization is an ionization technique that allows for fragmentation free analysis.

Mass selection


Mass analyzers separate the ions according to their mass-to-charge ratio
Mass-to-charge ratio
The mass-to-charge ratio ratio is a physical quantity that is widely used in the electrodynamics of charged particles, e.g. in electron optics and ion optics. It appears in the scientific fields of lithography, electron microscopy, cathode ray tubes, accelerator physics, nuclear physics, Auger...

. The following two laws govern the dynamics of charged particles in electric and magnetic fields in vacuum:
(Lorentz force law);
(Newton's second law of motion in 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 x B is the vector cross product of the ion velocity and the magnetic field

Equating the above expressions for the force applied to the ion yields:


This differential equation
Differential equation
A differential equation is a mathematical equation for an unknown function of one or several variables that relates the values of the function itself and its derivatives of various orders...

 is the classic equation of motion for charged particle
Charged particle
In physics, a charged particle is a particle with an electric charge. It may be either a subatomic particle or an ion. A collection of charged particles, or even a gas containing a proportion of charged particles, is called a plasma, which is called the fourth state of matter because its...

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 m/z, where z is the number of elementary charge
Elementary charge
The elementary charge, usually denoted as e, is the electric charge carried by a single proton, or equivalently, the absolute value of the electric charge carried by a single electron. This elementary charge is a fundamental physical constant. To avoid confusion over its sign, e is sometimes called...

s (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 analysers 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. Usually measured in ppm or milli mass unit
Milli mass unit
The milli mass unit or 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 tongue-breaking but formally more correct "milli unified atomic mass unit" and equivalent to 1/1000 of the...

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 an electric and/or magnetic field to affect the path and/or velocity
Velocity
In physics, velocity is speed in a given direction. Speed describes only how fast an object is moving, whereas velocity gives both the speed and direction of the object's motion. To have a constant velocity, an object must have a constant speed and motion in a constant direction. Constant ...

 of the charged
Electric charge
Electric charge is a physical property of matter that causes it to experience a force when near other electrically charged matter. Electric charge comes in two types, called positive and negative. Two positively charged substances, or objects, experience a mutual repulsive force, as do two...

 particles in some way.
As shown above, sector instrument
Sector instrument
A sector instrument is a general term for a class of mass spectrometer that uses a static electric or magnetic sector or some combination of the two as a mass analyzer. A popular combination of these sectors has been the BEB...

s 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
Time of flight describes a variety of methods that measure the time that it takes for an object, particle or acoustic, electromagnetic or other wave to travel a distance through a medium...

 (TOF) analyzer uses an electric field
Electric field
In physics, an electric field surrounds electrically charged particles and time-varying magnetic fields. The electric field depicts the force exerted on other electrically charged objects by the electrically charged particle the field is surrounding...

 to accelerate the ions through the same potential
Voltage
Voltage, otherwise known as electrical potential difference or electric tension is the difference in electric potential between two points — or the difference in electric potential energy per unit charge between two points...

, and then measures the time they take to reach the detector. If the particles all have the same charge, the kinetic energies
Kinetic energy
The kinetic energy of an object is the energy which it possesses due to its motion.It is defined as the work needed to accelerate a body of a given mass from rest to its stated velocity. Having gained this energy during its acceleration, the body maintains this kinetic energy unless its speed changes...

 will be identical, and their velocities
Velocity
In physics, velocity is speed in a given direction. Speed describes only how fast an object is moving, whereas velocity gives both the speed and direction of the object's motion. To have a constant velocity, an object must have a constant speed and motion in a constant direction. Constant ...

 will depend only on their mass
Mass
Mass can be defined as a quantitive measure of the resistance an object has to change in its velocity.In physics, mass commonly refers to any of the following three properties of matter, which have been shown experimentally to be equivalent:...

es. Lighter ions will reach the detector first.

Quadrupole mass filter



Quadrupole mass analyzer
Quadrupole mass analyzer
The quadrupole mass analyzer is one type of mass analyzer used in mass spectrometry. As the name implies, it consists of 4 circular rods, set parallel to each other. In a quadrupole mass spectrometer the quadrupole is the component of the instrument responsible for filtering sample ions, based on...

s use oscillating electrical fields to selectively stabilize or destabilize the paths of ions passing through a radio frequency
Radio frequency
Radio frequency is a rate of oscillation in the range of about 3 kHz to 300 GHz, which corresponds to the frequency of radio waves, and the alternating currents which carry radio signals...

 (RF) quadrupole
Quadrupole
A quadrupole or quadrapole is one of a sequence of configurations of—for example—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 reflecting various orders of complexity.-Mathematical...

 field created between 4 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
Quadrupole ion trap
A quadrupole ion trap exists in both linear and 3D varieties and refers to an ion trap that uses constant DC and radio frequency oscillating AC electric fields to trap ions. It is commonly used as a component of a mass spectrometer...

, 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 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
Tandem mass spectrometry, also known as MS/MS or MS2, involves multiple steps of mass spectrometry selection, with some form of fragmentation occurring in between the stages.-Tandem MS instruments:...

.

Three-dimensional quadrupole ion trap



The quadrupole ion trap
Quadrupole ion trap
A quadrupole ion trap exists in both linear and 3D varieties and refers to an ion trap that uses constant DC and radio frequency oscillating AC electric fields to trap ions. It is commonly used as a component of a mass spectrometer...

 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 a > b 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.

The cylindrical ion trap mass spectrometer is a derivative of the quadrupole ion trap mass spectrometer.

Linear quadrupole ion trap


A linear quadrupole ion trap 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.

Orbitrap



Very similar nonmagnetic FTMS has been performed, where ions are electrostatically 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 of the recorded image currents.

Similar to Fourier transform ion cyclotron resonance
Fourier transform ion cyclotron resonance
Fourier transform ion cyclotron resonance mass spectrometry, also known as Fourier transform mass spectrometry, is a type of mass analyzer for determining the mass-to-charge ratio of ions based on the cyclotron frequency of the ions in a fixed magnetic field...

 mass spectrometers, 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
Fourier transform ion cyclotron resonance mass spectrometry, also known as Fourier transform mass spectrometry, is a type of mass analyzer for determining the mass-to-charge ratio of ions based on the cyclotron frequency of the ions in a fixed magnetic field...

 MS, measures mass by detecting the image current produced by ions cyclotron
Cyclotron
In technology, a cyclotron is a type of particle accelerator. In physics, the cyclotron frequency or gyrofrequency is the frequency of a charged particle moving perpendicularly to the direction of a uniform magnetic field, i.e. a magnetic field of constant magnitude and direction...

ing in the presence of a magnetic field. Instead of measuring the deflection of ions with a detector such as an electron multiplier
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...

, the ions are injected into a Penning trap
Penning trap
Penning traps are devices for the storage of charged particles using a homogeneous static magnetic field and a spatially inhomogeneous static electric field. This kind of trap is particularly well suited to precision measurements of properties of ions and stable subatomic particles which have...

 (a static electric/magnetic ion trap
Ion trap
An ion trap is a combination of electric or magnetic fields that captures ions in a region of a vacuum system or tube. Ion traps have a number of scientific uses such as mass spectrometery and trapping ions while the ion's quantum state is manipulated...

) 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
Deconvolution
In mathematics, deconvolution is an algorithm-based process used to reverse the effects of convolution on recorded data. The concept of deconvolution is widely used in the techniques of signal processing and image processing...

 by performing a Fourier transform
Fourier transform
In mathematics, Fourier analysis is a subject area which grew from the study of Fourier series. The subject began with the study of the way general functions may be represented by sums of simpler trigonometric functions...

 on the signal. FTMS has the advantage of high sensitivity (since each ion is "counted" more than once) and much higher resolution
Resolution (mass spectrometry)
In mass spectrometry, resolution measures of the ability to distinguish two peaks of slightly different mass-to-charge ratios ΔM, in a mass spectrum.- Resolution and Resolving Power :...

 and thus precision.

Ion cyclotron resonance
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 transform ion cyclotron resonance mass spectrometers...

 (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
Penning trap
Penning traps are devices for the storage of charged particles using a homogeneous static magnetic field and a spatially inhomogeneous static electric field. This kind of trap is particularly well suited to precision measurements of properties of ions and stable subatomic particles which have...

 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
Mass spectrum
A mass spectrum is an intensity vs. m/z plot representing a chemical analysis. Hence, the mass spectrum of a sample is a pattern representing the distribution of ions by mass in a sample. It is a histogram usually acquired using an instrument called a mass spectrometer...

, a record of ions as a function of m/Q.

Typically, some type of electron multiplier
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...

 is used, though other detectors including Faraday cup
Faraday cup
A Faraday cup is a metal 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...

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 detector
Microchannel plate detector
A micro-channel plate is a planar component used for detection of particles and impinging radiation . It is closely related to an electron multiplier, as both intensify single particles or photons by the multiplication of electrons via secondary emission...

s are commonly used in modern commercial instruments. In FTMS and Orbitrap
Orbitrap
An orbitrap is a type of mass spectrometer invented by Alexander Makarov. It consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution....

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 DC 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
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...

 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
In Mass spectrometry, Collision-induced dissociation , referred to by some as collisionally activated dissociation , is a mechanism by which to fragment molecular ions in the gas phase. The molecular ions are usually accelerated by some electrical potential to high kinetic energy and then allowed...

 (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
Quadrupole ion trap
A quadrupole ion trap exists in both linear and 3D varieties and refers to an ion trap that uses constant DC and radio frequency oscillating AC electric fields to trap ions. It is commonly used as a component of a mass spectrometer...

. There are various methods for fragmenting
Fragmentation (chemistry)
Fragmentation is a type of chemical dissociation. Fragmentation of a molecule can take place by a process of heterolysis or homolysis.It is a phenomenon observed in mass spectrometry where it is used as a tool to find the structural formula of a molecule, process called structural elucidation.It...

 molecules for tandem MS, including collision-induced dissociation
Collision-induced dissociation
In Mass spectrometry, Collision-induced dissociation , referred to by some as collisionally activated dissociation , is a mechanism by which to fragment molecular ions in the gas phase. The molecular ions are usually accelerated by some electrical potential to high kinetic energy and then allowed...

 (CID), electron capture dissociation
Electron capture dissociation
Electron-capture dissociation is a method of fragmenting gas phase ions for tandem mass spectrometric analysis . ECD involves the direct introduction of low energy electrons to trapped gas phase ions...

 (ECD), electron transfer dissociation
Electron transfer dissociation
Electron-transfer dissociation is a method of fragmenting ions in a mass spectrometer. Similar to electron-capture dissociation, ETD induces fragmentation of cations by transferring electrons to them. It was invented by Donald F. Hunt, Joshua Coon, John E. P...

 (ETD), infrared multiphoton dissociation
Infrared multiphoton dissociation
Infrared multiphoton dissociation is a technique used in mass spectrometry to fragment molecules in the gas phase usually for structural analysis of the original molecule. -How it works:...

 (IRMPD), blackbody infrared radiative dissociation
Blackbody infrared radiative dissociation
In mass spectrometry blackbody infrared radiative dissociation is a method for fragmenting gas phase ions for tandem mass spectrometric analysis . BIRD uses the light from black body radiation to thermally excite the ions until a bond breaks...

 (BIRD), electron-detachment dissociation
Electron-detachment dissociation
Electron-detachment dissociation is a method for fragmenting anionic species in mass spectrometry....

 (EDD) and surface-induced dissociation
Surface-induced dissociation
Surface-induced dissociation is a technique used in mass spectrometry to fragment molecular ions in the gas phaseby collision of an ion with a surface under high vacuum....

 (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)
Selected reaction monitoring
Selected reaction monitoring is a method used in tandem mass spectrometry in which an ion of a particular mass is selected in the first stage of a tandem mass spectrometer and an ion product of a fragmentation reaction of the precursor ion is selected in the second mass spectrometer stage for...

 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
Duty cycle
In engineering, the duty cycle of a machine or system is the time that it spends in an active state as a fraction of the total time under consideration....

 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
Radiocarbon dating
Radiocarbon dating is a radiometric dating method that uses the naturally occurring radioisotope carbon-14 to estimate the age of carbon-bearing materials up to about 58,000 to 62,000 years. Raw, i.e. uncalibrated, radiocarbon ages are usually reported in radiocarbon years "Before Present" ,...

 is Accelerator Mass Spectrometry
Accelerator mass spectrometry
Accelerator mass spectrometry differs from other forms of mass spectrometry in that it 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 rare isotope from an abundant...

 (AMS), which uses very high voltages, usually in the mega-volt range, to accelerate negative ions into a type of tandem mass spectrometer.

Common mass spectrometer configurations and techniques


When a specific configuration of source, analyzer, and detector becomes conventional in practice, often a compound acronym arises to designate it, and the compound acronym may be better known among nonspectrometrists than the component acronyms. The epitome of this is MALDI-TOF, which simply refers to combining a matrix-assisted laser desorption/ionization
Matrix-assisted laser desorption/ionization
Matrix-assisted laser desorption/ionization is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules and large organic molecules , which tend to be fragile and fragment when ionized by more conventional ionization methods...

 source with a time-of-flight
Time-of-flight
Time of flight describes a variety of methods that measure the time that it takes for an object, particle or acoustic, electromagnetic or other wave to travel a distance through a medium...

 mass analyzer. The MALDI-TOF moniker is more widely recognized by the non-mass spectrometrists than MALDI or TOF individually. Other examples include inductively coupled plasma-mass spectrometry (ICP-MS)
ICP-MS
Inductively coupled plasma mass spectrometry is a type of mass spectrometry that is highly sensitive and capable of the determination of a range of metals and several non-metals at concentrations below one part in 1012...

, accelerator mass spectrometry (AMS)
Accelerator mass spectrometry
Accelerator mass spectrometry differs from other forms of mass spectrometry in that it 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 rare isotope from an abundant...

, Thermal ionization-mass spectrometry (TIMS) and spark source mass spectrometry (SSMS)
Spark ionization
Spark ionization is a method used to produce gas phase ions from a solid sample. The prepared solid sample is vaporized and partially ionized by an intermittent discharge or spark. This technique is primarily used in the field of mass spectrometry...

. Sometimes the use of the generic "MS" actually connotes a very specific mass analyzer and detection system, as is the case with AMS, which is always sector based.

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 (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.

Chromatographic 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
Chromatography
Chromatography is the collective term for a set of laboratory techniques for the separation of mixtures....

 separation techniques.

Gas chromatography




A common combination is gas
Gas
Gas is one of the three classical states of matter . Near absolute zero, a substance exists as a solid. As heat is added to this substance it melts into a liquid at its melting point , boils into a gas at its boiling point, and if heated high enough would enter a plasma state in which the electrons...

 chromatography-mass spectrometry (GC/MS or GC-MS). In this technique, a gas chromatograph is used to separate different compounds. This stream of separated compounds is fed online into the ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

 source, a metal
Metal
A metal , is an element, compound, or alloy that is a good conductor of both electricity and heat. Metals are usually malleable and shiny, that is they reflect most of incident light...

lic filament to which voltage
Voltage
Voltage, otherwise known as electrical potential difference or electric tension is the difference in electric potential between two points — or the difference in electric potential energy per unit charge between two points...

 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.

Liquid chromatography



Similar 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
Water is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state . Water also exists in a...

 and organic solvent
Solvent
A solvent is a liquid, solid, or gas that dissolves another solid, liquid, or gaseous solute, resulting in a solution that is soluble in a certain volume of solvent at a specified temperature...

s, instead of gas and the ions fragments cannot yield predictable patterns. Most commonly, an electrospray ionization
Electrospray ionization
Electrospray ionization is a technique used in mass spectrometry to produce ions. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized...

 source is used in LC/MS. There are also some newly developed ionization techniques like laser spray
Laser spray
Laser spray ionization refers to one of several methods for creating ions using a laser interacting with a spray of neutral particles or ablating material to create a plume of charged particles...

.

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
Duty cycle
In engineering, the duty cycle of a machine or system is the time that it spends in an active state as a fraction of the total time under consideration....

 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
Liquid chromatography-mass spectrometry
Liquid chromatography–mass spectrometry is an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry. LC-MS is a powerful technique used for many applications which has very high...

.

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
Mass spectrum
A mass spectrum is an intensity vs. m/z plot representing a chemical analysis. Hence, the mass spectrum of a sample is a pattern representing the distribution of ions by mass in a sample. It is a histogram usually acquired using an instrument called a mass spectrometer...

.

Certain types of mass spectrometry data are best represented as a mass chromatogram
Mass chromatogram
A mass chromatogram is a representation of mass spectrometry data as a chromatogram, where the x-axis represents time and the y-axis represents signal intensity. The source data contains mass information; however, it is not graphically represented in a mass chromatogram in favor of visualizing...

. Types of chromatograms include selected ion monitoring (SIM), total ion current (TIC), and selected reaction monitoring chromatogram (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


Basics

Mass spectrometry data analysis is a complicated subject that is very specific to the type of experiment producing the data. There are general subdivisions of data that 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.

By understanding the origin of a sample, certain expectations can be assumed as to 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 relatively crudely prepared biological sample will probably contain a certain amount of salt, which may form adduct
Adduct
An adduct is a product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species...

s with the analyte molecules in certain analyses.

Results can also depend heavily on how the sample was prepared 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.

The greatest source of trouble when non-mass spectrometrists try to conduct mass spectrometry on their own or collaborate with a mass spectrometrist is inadequate definition of the research goal of the experiment. Adequate definition of the experimental goal is a prerequisite for collecting the proper data and successfully interpreting it. Among the determinations that can be achieved with mass spectrometry are molecular mass, molecular structure, and sample purity. Each of these questions requires a different experimental procedure. Simply asking for a "mass spec" will most likely not answer the real question at hand.

Interpretation of mass spectra

Since the precise structure
Chemical structure
A chemical structure includes molecular geometry, electronic structure and crystal structure of molecules. Molecular geometry refers to the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together. Molecular geometry can range from the very simple, such as...

 or peptide sequence
Peptide sequence
Peptide sequence or amino acid sequence is the order in which amino acid residues, connected by peptide bonds, lie in the chain in peptides and proteins. The sequence is generally reported from the N-terminal end containing free amino group to the C-terminal end containing free carboxyl group...

 of a molecule is deciphered through the set of fragment masses, the interpretation of mass spectra
Mass spectrum
A mass spectrum is an intensity vs. m/z plot representing a chemical analysis. Hence, the mass spectrum of a sample is a pattern representing the distribution of ions by mass in a sample. It is a histogram usually acquired using an instrument called a mass spectrometer...

 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 the search comes up empty, then manual interpretation or software assisted interpretation of mass spectra
Mass spectrometry software
Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry.- MS/MS peptide identification :...

 are performed. Computer simulation of ionization
Ionization
Ionization is the process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This is often confused with dissociation. A substance may dissociate without necessarily producing ions. As an example, the molecules of table sugar...

 and fragmentation processes occurring in mass spectrometer is the primary tool for assigning structure or peptide sequence to a molecule. An a priori structural information is fragmented in silico
In silico
In silico is an expression used to mean "performed on computer or via computer simulation." The phrase was coined in 1989 as an analogy to the Latin phrases in vivo and in vitro which are commonly used in biology and refer to experiments done in living organisms and outside of living organisms,...

 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
Mass spectrometry software
Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry.- MS/MS peptide identification :...

 taking advantage of this idea has been developed for both small molecules and proteins
Peptide mass fingerprinting
Peptide mass fingerprinting is an analytical technique for protein identification that was developed in 1993 by several groups independently. In this method, the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass...

.

Another way of interpreting mass spectra involves 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. More precise mass figures significantly reduce the number of candidate molecular formulas, albeit each can still represent large number of structurally diverse compounds. A computer algorithm called formula generator calculates all molecular formulas that theoretically fit a given mass 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
Tandem mass spectrometry
Tandem mass spectrometry, also known as MS/MS or MS2, involves multiple steps of mass spectrometry selection, with some form of fragmentation occurring in between the stages.-Tandem MS instruments:...

 of the molecule under investigation against a library of the product-ion spectra of structurally characterized precursor ions.

Isotope ratio MS: isotope dating and tracking




Mass spectrometry is also used to determine the isotopic
Isotope
Isotopes are variants of atoms of a particular chemical element, which have differing numbers of neutrons. Atoms of a particular element by definition must contain the same number of protons but may have a distinct number of neutrons which differs from atom to atom, without changing the designation...

 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
Faraday cup
A Faraday cup is a metal 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...

s which convert particle impacts to electric current
Electric current
Electric current is a flow of electric charge through a medium.This charge is typically carried by moving electrons in a conductor such as wire...

. A fast on-line analysis of deuterium
Deuterium
Deuterium, also called heavy hydrogen, is one of two stable isotopes of hydrogen. It has a natural abundance in Earth's oceans of about one atom in of hydrogen . Deuterium accounts for approximately 0.0156% of all naturally occurring hydrogen in Earth's oceans, while the most common isotope ...

 content of water can be done using Flowing afterglow mass spectrometry
Flowing afterglow mass spectrometry
Flowing-afterglow mass spectrometry, FA-MS, is a sensitive and quantitative mass spectrometry analytical approach that offers a route to on-line, real-time deuterium abundance measurements in water vapour in breath and above aqueous liquids, including urine and serum...

, FA-MS. Probably the most sensitive and accurate mass spectrometer for this purpose is the accelerator mass spectrometer
Accelerator mass spectrometry
Accelerator mass spectrometry differs from other forms of mass spectrometry in that it 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 rare isotope from an abundant...

 (AMS). 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)

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 selected ion flow tube mass spectrometry
Selected ion flow tube mass spectrometry, SIFT-MS, is a quantitative mass spectrometry technique for trace gas analysis which involves the chemical ionization of trace volatile compounds by selected positive precursor ions during a well-defined time period along a flow tube...

 (SIFT-MS), and proton transfer reaction (PTR-MS), are variants of chemical ionization
Chemical ionization
Chemical ionization is an ionization technique used in mass spectrometry. Chemical ionization is a lower energy process than electron ionization. The lower energy yields less fragmentation, and usually a simpler spectrum...

 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.

Atom probe



An atom probe
Atom probe
The atom probe is a microscope used in material science that was invented in 1967 by Erwin Wilhelm Müller, J. A. Panitz, and S. Brooks McLane. The atom probe is closely related to the method of Field Ion Microscopy, which is the first microscopic method to achieve atomic resolution, occurring in...

 is an instrument that combines time-of-flight
Time-of-flight
Time of flight describes a variety of methods that measure the time that it takes for an object, particle or acoustic, electromagnetic or other wave to travel a distance through a medium...

 mass spectrometry and field ion microscopy
Field ion microscope
Field ion microscopy is an analytical technique used in materials science. The field ion microscope is a type of microscope that can be used to image the arrangement of atoms at the surface of a sharp metal tip....

 (FIM) 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
Liquid chromatography-mass spectrometry
Liquid chromatography–mass spectrometry is an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry. LC-MS is a powerful technique used for many applications which has very high...

 with a triple quadrupole mass spectrometer
Quadrupole mass analyzer
The quadrupole mass analyzer is one type of mass analyzer used in mass spectrometry. As the name implies, it consists of 4 circular rods, set parallel to each other. In a quadrupole mass spectrometer the quadrupole is the component of the instrument responsible for filtering sample ions, based on...

. 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
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 is required, or smoothing, in which a "smooth" function...

 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
Microdosing
Microdosing is a technique for studying the behaviour of drugs in humans through the administration of doses so low they are unlikely to produce whole-body effects, but high enough to allow the cellular response to be studied...

 studies, which are seen as a promising alternative to animal experimentation.

Protein characterization



Mass spectrometry is an important emerging method for the characterization and sequencing
Protein sequencing
Protein sequencing is a technique to determine the amino acid sequence of a protein, as well as which conformation the protein adopts and the extent to which it is complexed with any non-peptide molecules...

 of proteins. The two primary methods for ionization of whole proteins are electrospray ionization
Electrospray ionization
Electrospray ionization is a technique used in mass spectrometry to produce ions. It is especially useful in producing ions from macromolecules because it overcomes the propensity of these molecules to fragment when ionized...

 (ESI) and matrix-assisted laser desorption/ionization
Matrix-assisted laser desorption/ionization
Matrix-assisted laser desorption/ionization is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules and large organic molecules , which tend to be fragile and fragment when ionized by more conventional ionization methods...

 (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
Top-down proteomics
Top-down proteomics is a method of protein identification that uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry analysis. The name is derived from the similar approach to DNA seqencing...

" strategy of protein analysis. In the second, proteins are enzymatically digested into smaller peptides using protease
Protease
A protease is any enzyme that conducts proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein....

s such as trypsin
Trypsin
Trypsin is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. Trypsin is produced in the pancreas as the inactive proenzyme trypsinogen. Trypsin cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine, except when...

 or pepsin
Pepsin
Pepsin is an enzyme whose precursor form is released by the chief cells in the stomach and that degrades food proteins into peptides. It was discovered in 1836 by Theodor Schwann who also coined its name from the Greek word pepsis, meaning digestion...

, either in solution
Solution
In chemistry, a solution is a homogeneous mixture composed of only one phase. In such a mixture, a solute is dissolved in another substance, known as a solvent. The solvent does the dissolving.- Types of solutions :...

 or in gel
In-gel digestion
The in-gel digestion is part of the sample preparation for the mass spectrometric identification of proteins in course of proteomic analysis. The method was introduced 1992 by Rosenfeld...

 after electrophoretic
Electrophoresis
Electrophoresis, also called cataphoresis, is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field. This electrokinetic phenomenon was observed for the first time in 1807 by Reuss , who noticed that the application of a constant electric...

 separation. Other proteolytic agents are also used. The collection of peptide products are then introduced 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
Peptide mass fingerprinting
Peptide mass fingerprinting is an analytical technique for protein identification that was developed in 1993 by several groups independently. In this method, the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass...

 (PMF), if the identification is performed using the sequence data determined in tandem MS
Tandem mass spectrometry
Tandem mass spectrometry, also known as MS/MS or MS2, involves multiple steps of mass spectrometry selection, with some form of fragmentation occurring in between the stages.-Tandem MS instruments:...

 analysis it is called de novo sequencing. These procedures of protein analysis are also referred to as the "bottom-up
Bottom-up proteomics
Bottom-up proteomics is a common method to identify proteins and characterize their amino acid sequences and post-translational modifications by proteolytic digestion of proteins prior to analysis by mass spectrometry. The proteins may first be purified by a method such as gel electrophoresis...

" approach.

Glycan analysis


Mass spectrometry (MS), with its low sample requirement and high sensitivity, has been the predominantly used in glycobiology
Glycobiology
Defined in the broadest sense, glycobiology is the study of the structure, biosynthesis, and biology of saccharides that are widely distributed in nature...

 for characterization and elucidation of glycan structures. Mass spectrometry provides a complementary method to HPLC
High-performance liquid chromatography
High-performance liquid chromatography , HPLC, is a chromatographic technique that can separate a mixture of compounds and is used in biochemistry and analytical chemistry to identify, quantify and purify the individual components of the mixture.HPLC typically utilizes different types of stationary...

 for the analysis of glycans. Intact glycans may be detected directly as singly charged ions by matrix-assisted laser desorption/ionization mass spectrometry
Matrix-assisted laser desorption/ionization
Matrix-assisted laser desorption/ionization is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules and large organic molecules , which tend to be fragile and fragment when ionized by more conventional ionization methods...

 (MALDI-MS) or, following permethylation or peracetylation, by fast atom bombardment mass spectrometry
Fast atom bombardment
Fast atom bombardment is an ionization technique used in mass spectrometry. The material to be analyzed is mixed with a non-volatile chemical protection environment called a matrix and is bombarded under vacuum with a high energy beam of atoms. The atoms are typically from an inert gas such as...

 (FAB-MS). Electrospray ionization mass spectrometry (ESI-MS) also gives good signals for the smaller glycans. Various free and commercial software are now available which interpret MS data and aid in Glycan structure characterization.

Space exploration


As a standard method for analysis, mass spectrometers have reached other planets and moons. Two were taken to Mars
Mars
Mars is the fourth planet from the Sun in the Solar System. The planet is named after the Roman god of war, Mars. It is often described as the "Red Planet", as the iron oxide prevalent on its surface gives it a reddish appearance...

 by the Viking program
Viking program
The Viking program consisted of a pair of American space probes sent to Mars, Viking 1 and Viking 2. Each spacecraft was composed of two main parts, an orbiter designed to photograph the surface of Mars from orbit, and a lander designed to study the planet from the surface...

. In early 2005 the Cassini–Huygens mission delivered a specialized GC-MS instrument aboard the Huygens probe
Huygens probe
The Huygens probe was an atmospheric entry probe carried to Saturn's moon Titan as part of the Cassini–Huygens mission. The probe was supplied by the European Space Agency and named after the Dutch 17th century astronomer Christiaan Huygens....

 through the atmosphere of Titan
Titan (moon)
Titan , or Saturn VI, is the largest moon of Saturn, the only natural satellite known to have a dense atmosphere, and the only object other than Earth for which clear evidence of stable bodies of surface liquid has been found....

, the largest moon of the planet Saturn
Saturn
Saturn is the sixth planet from the Sun and the second largest planet in the Solar System, after Jupiter. Saturn is named after the Roman god Saturn, equated to the Greek Cronus , the Babylonian Ninurta and the Hindu Shani. Saturn's astronomical symbol represents the Roman god's sickle.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 onboard the Cassini–Huygens spacecraft is an ion and neutral mass spectrometer which has been taking measurements of Titan's atmospheric composition as well as the composition of Enceladus
Enceladus (moon)
Enceladus is the sixth-largest of the moons of Saturn. It was discovered in 1789 by William Herschel. Until the two Voyager spacecraft passed near it in the early 1980s very little was known about this small moon besides the identification of water ice on its surface...

' plumes. A Thermal and Evolved Gas Analyzer
Thermal and Evolved Gas Analyzer
The Thermal and Evolved Gas Analyzer is a scientific instrument aboard the Phoenix spacecraft. TEGA's design is based on experience gained from the failed Mars Polar Lander. Soil samples taken from the Martian surface by the robot arm are eventually delivered to the TEGA, where they are heated in...

 mass spectrometer was carried by the Mars Phoenix Lander
Phoenix (spacecraft)
Phoenix was a robotic spacecraft on a space exploration mission on Mars under the Mars Scout Program. The Phoenix lander descended on Mars on May 25, 2008...

 launched in 2007.

Mass spectrometers are also widely used in space missions to measure the composition of plasmas. For example, the Cassini spacecraft carries the Cassini Plasma Spectrometer (CAPS), which measures the mass of ions in Saturn's magnetosphere
Magnetosphere
A magnetosphere is formed when a stream of charged particles, such as the solar wind, interacts with and is deflected by the intrinsic magnetic field of a planet or similar body. Earth is surrounded by a magnetosphere, as are the other planets with intrinsic magnetic fields: Mercury, Jupiter,...

.

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
Anesthesia
Anesthesia, or anaesthesia , traditionally meant the condition of having sensation blocked or temporarily taken away...

 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
Atomic mass unit
The unified atomic mass unit or dalton is a unit that is used for indicating mass on an atomic or molecular scale. It is defined as one twelfth of the rest mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state, and has a value of...

, fragmentation of some of the heavier molecules negated the need for a higher detection limit.

See also


  • Mass spectrometry software
    Mass spectrometry software
    Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry.- MS/MS peptide identification :...

  • Electron spectrometer
    Electron spectrometer
    In an Electron spectrometer, an incoming beam of electrons is bent with electric or magnetic fields. As higher energy electrons will be bent less by the beam, this produces a spatially distributed range of energies....

  • Atom probe
    Atom probe
    The atom probe is a microscope used in material science that was invented in 1967 by Erwin Wilhelm Müller, J. A. Panitz, and S. Brooks McLane. The atom probe is closely related to the method of Field Ion Microscopy, which is the first microscopic method to achieve atomic resolution, occurring in...

  • Calutron
    Calutron
    A calutron is a mass spectrometer used for separating the isotopes of uranium. It was developed by Ernest O. Lawrence during the Manhattan Project and was similar to the cyclotron invented by Lawrence. Its name is a concatenation of Cal. U.-tron, in tribute to the University of California,...

  • Helium mass spectrometer
    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 plants. It typically uses a vacuum chamber in which a...

  • Ion attachment mass spectrometry
  • MALDI imaging
    MALDI imaging
    MALDI imaging is the use of matrix-assisted laser desorption ionization as a mass spectrometry imaging technique in which the sample, often a thin tissue section, is moved in two dimensions while the mass spectrum is recorded.-Applications:...

  • Mass spectrometry imaging
    Mass spectrometry imaging
    Mass spectrometry imaging is a technique used in mass spectrometry to visualize the spatial distribution of e.g. compounds, biomarker, metabolites, peptides or proteins by their molecular masses...

  • Desorption atmospheric pressure photoionization
    Desorption atmospheric pressure photoionization
    Desorption atmospheric pressure photoionization is an atmospheric-pressure ionization technique for mass spectrometry. DAPPI enables direct analysis of solid samples without pretreatment and analysis of samples deposited on surfaces by means of a jet of hot solvent vapour and vacuum ultraviolet...

  • Membrane introduction mass spectrometry
    Membrane introduction mass spectrometry
    Membrane-introduction mass spectrometry is a method of introducing analytes into the mass spectrometer's vacuum chamber via a semipermeable membrane. Usually a thin, gas permeable, hydrophobic membrane is used, for example polydimethylsiloxane. Samples can be almost any fluid including water,...

  • Secondary ionisation
  • Taylor cone
    Taylor cone
    A Taylor cone refers to the cone observed in electrospinning, electrospraying and hydrodynamic spray processes from which a jet of charged particles emanates above a threshold voltage...

  • Reflectron
    Reflectron
    A reflectron is a type of time-of-flight mass spectrometer 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 reverse the direction of travel of the ions entering it...



External links