Mass spectrometry

Mass spectrometry is an analytical technique used to measure the mass-to-charge ratio (m/z) of ions. It is most generally used to find the composition of a physical sample by generating a mass spectrum representing the masses of sample components. The technique has several applications, including:

1. identifying unknown compounds by the mass of the compound and/or fragments thereof.
2. determining the isotopic composition of one or more elements in a compound.
3. determining the structure of compounds by observing the fragmentation of the compound.
4. quantitating the amount of a compound in a sample using carefully designed methods (mass spectrometry is not inherently quantitative).
5. studying the fundamentals of gas phase ion chemistry (the chemistry of ions and neutrals in vacuum).
6. determining other physical, chemical or even biological properties of compounds with a variety of other approaches.

A mass spectrometer is a device used for mass spectrometry, and produces a mass spectrum of a sample to find its composition. This is normally achieved by ionizing the sample and separating ions of differing masses and recording their relative abundance by measuring intensities of ion flux. A typical mass spectrometer comprises three parts: an ion source, a mass analyzer, and a detector.

How it works: A simple example

Different chemicals have different masses, and this fact is used in a mass spectrometer to determine what chemicals are present in a sample. For example, table salt (NaCl), is vaporized (turned into gas) and ionized (broken down) into electrically charged particles, called ions, in the first part of the mass spectrometer. The sodium ions and chloride ions have specific atomic weights. They also have a charge, which means that they can be moved under the influence of an electric field or magnetic field. These ions are then sent into an ion acceleration chamber and passed through a slit in a metal sheet. A magnetic field is applied to the chamber, which pulls on each ion equally and deflects them (makes them curve instead of travelling straight) onto a detector. The lighter ions deflect farther than the heavy ions because the force on each ion is equal but their masses are not (this is derived from the equation $F=ma$ which states that if the force remains the same, the mass and acceleration are inversely proportional). The detector measures exactly how far each ion has been deflected, and from this measurement, the ion's 'mass to charge ratio' can be worked out. From this information it is possible to determine with a high level of certainty what the chemical composition of the original sample was.

This example was of a sector instrument, however there are many types of mass spectrometers that not only analyze the ions differently but produce different types of ions; however they all use electric and magnetic fields to change the path of ions in some way.

Instrumentation

Ion source

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 or electrical fields to the mass analyzer.

Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the analyte is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp). Inductively coupled plasma sources are used primarily for metal analysis on a wide array of samples types. Others include fast atom bombardment (FAB), thermospray, atmospheric pressure chemical ionization (APCI), secondary ion mass spectrometry (SIMS) and thermal ionisation.

Mass analyzer

Mass analyzers separate the ions according to their mass-to-charge ratio(m/z). There are many types of mass analyzers. Usually they are categorized based on the principles of operation.

Sector MS: It uses an electric and/or magnetic field to affect the path and/or velocity of the charged particles in some way. The force exerted by electric and magnetic fields are defined by the Lorentz force law:

$\mathbf {F} =q(\mathbf {E} +\mathbf {v} \times \mathbf {B} ),$

where E is the electric field strength, B is the magnetic field induction, q is the charge of the particle, v is its current velocity (expressed as a vector), and × is the cross product. All mass analyzers use the Lorentz forces in some way either statically or dynamically in mass-to-charge determination.

As shown above, sector instruments change the direction of ions that are flying through the mass analyzer. The ions enter a magnetic or electric field which bends the ion paths depending on their mass-to-charge ratios (m/z), deflecting the more charged and faster-moving, lighter ions more. The ions eventually reach the detector and their relative abundances are measured. The analyzer can be used to select a narrow range of m/z's or to scan through a range of m/z's to catalog the ions present.

Besides the original magnetic-sector analyzers, several other types of analyzer are now more common, including time-of-flight, quadrupole ion trap, quadrupole and Fourier transform ion cyclotron resonance mass analyzers.

TOFMS: Perhaps the easiest to understand is the Time-of-flight (TOF) analyzer. It boosts ions to the same kinetic energy by passage through an electric field and then measures the times they take to reach the detector. While the nominal kinetic energy of all the ions is the same, the resultant velocity is different, thereby causing lighter ions (and also more highly charged ions) to reach the detector first.

QMS: Quadrupole mass analyzers use oscillating electrical fields to selectively stabilize or destabilize ions passing through a RF quadrupole field.

QIT: The quadrupole ion trap works on the same physical principles as the QMS, but the ions are trapped and sequentially ejected. Ions are created and trapped in a mainly quadrupole RF potential and separated by m/z, non-destructively or destructively. There are many mass/charge separation and isolation methods but 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. 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.

See also the main article on quadrupole ion trap mass spectrometer

Linear QIT: In the linear quadrupole ion trap the ions are trapped in a 2D quadrupole field instead of the 3D quadrupole field of the QIT.

FTMS: Fourier transform mass spectrometry or more precisely Fourier transform ion cyclotron resonance mass spectrometry measures mass by detecting the image current produced by ions cyclotroning in the presence of a magnetic field. Instead of measuring the deflection of ions with a detector such as a electron multiplier, the ions are injected into a Penning trap (a static electric/magnetic ion trap) 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 cyclical signal. Since the frequency of the ions' cycling is determined by its mass to charge ratio, this can be deconvoluted by performing a Fourier transform on the signal. FTMS has the advantage of improved sensitivity (since each ion is 'counted' more than once) as well as much higher resolution and thus precision.

See also the main article on Fourier transform ion cyclotron resonance

ICR: Ion cyclotron resonance is an older mass analysis technique that is similar to FTMS above except ions are detected with a traditional detector. Ions trapped in a Penning trap are excited by an RF electric field until they impact the wall of the trap where the detector is located with ions of different mass being resolved in time.

Orbitrap: Orbitraps are the most recently introduced mass analysers (commercially available since 2005). Ions are electrostatically trapped in an orbit around a central, spindle-shaped electrode. They perform two kinds of movements in parallel: First, they cycle in an orbit around the central electrode. Second, they also move back and forth along the axis of the central electrode. Thus, the ion movement resembles a ring that oscillates along the axis of the spindle. This oscillation generates an image current in detector plates which is recorded. The frequencies of these image currents depend on the mass to charge ratios of the ions in the Orbitrap. Mass spectra are obtained by Fourier transformation of the recorded image currents. Similar to Fourier transform ion cyclotron resonance mass spectrometers, Orbitraps have a high mass accuracy, high sensitivity and an increased dynamic range.

Each analyzer type has its strengths and weaknesses. In addition, there are many more less-common mass analyzers. Many mass spectrometers use two or more mass analyzers for tandem mass spectrometry (MS/MS).

Detector

The final element of the mass spectrometer is the detector. The detector records the charge induced or 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/z) will produce a mass spectrum, a record of how many ions of each m/z are present.

Typically, some types of electron multiplier is used, though other detectors (such as Faraday cups) have been used. Because the number of ions leaving the mass analyzer at a particular instant is typically quite small, significant amplification is often necessary to get a signal. Microchannel Plate Detectors are commonly used in modern commercial instruments. In FTMS, the detector consists of a pair of metal plates within the mass analyzer region which the ions only pass near. No DC current is produced, only a weak AC image current is produced in a circuit between the plates.

Hyphenated MS

Gas chromatography/MS

See also the main article on Gas chromatography-mass spectrometry

A common form of mass spectrometry is gas chromatography-mass spectrometry (GC/MS or GC-MS). In this technique, a gas chromatograph is used to separate compounds. This stream of separated compounds is fed on-line into the ion source, a metallic filament to which voltage 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 analyser and are eventually detected.

Liquid chromatography/MS

See also the main article on Liquid chromatography-mass spectrometry

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 combination of water and organic solvents, instead of gas. Most commonly, an electrospray ionization source is used in LC/MS.

IMS/MS

Ion mobility spectrometry/mass spectrometry is a technique where ions are first separated by drift time through some pressure of neutral gas given an electrical potential gradient before being introduced into a mass spectrometer. The drift time is a measure of the radius relative to the charge of the ion. The duty cycle of IMS (time over which the experiment takes place) is longer than most mass spectrometers 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. Note, however, that the duty cycle of IMS is short relative to liquid chromatography or gas chromatography separations and can thus be coupled to such techniques producing triply hyphenated techniques such as LC/IMS/MS.

Tandem MS (MS/MS)

Tandem mass spectrometry involves multiple steps of mass selection or analysis, usually separated by some form of fragmentation. A tandem mass spectrometer is one capable of multiple rounds of mass spectrometry. For example, one mass analyzer can isolate one peptide 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 (CID). A third mass analyzer then catalogs the fragments produced from the peptides. Tandem MS can also be done in a single mass analyzer over time as in a quadrupole ion trap. There are various methods for fragmenting molecules for tandem MS, including collision-induced dissociation (CID), electron capture dissociation (ECD), electron transfer dissociation (ETD), infrared multiphoton dissociation (IRMPD) and blackbody infrared radiative dissociation (BIRD).

Data and Analysis

Data Representations

Mass spectrometry produces many different types of data. The most ubiquitous data representation is the mass spectrum. Certain types of mass spectrometry data are best represented as a mass chromatogram. Mass chromatograms can represent a single ion chromatogram (SIC) (aka single ion monitoring (SIM)), a total ion chromatogram (TIC) or a multiple reaction monitoring chromatogram (MRM) among many other types of mass chromatograms. Other types of mass spectrometry data are well represented as a contour map which represent mass-to-charge on one axis, intensity on another and an additional experimental parameter (often time) on the third axis, thus producing a three dimensional surface.

Data Analysis

Basics

Mass spectrometry data analysis is a complicated subject matter that is very specific to the type of experiment producing the data. There are several general subdivisions of data that are fundamental to beginning to understand any data. These include: positive vs. negative ion mode, molecular ions vs. fragment ions, even electron species vs. odd electron species, etc.

Here are some relevant questions that a mass spectrometrist might ask on being shown a mass spectrum without any explanation:

Is the data positive ion mode or negative ion mode data?

It is very important to understand if the ions observed are negatively or positively charged. For one this is often important in determining the neutral mass but it also indicates something about the nature of the molecules.

What ion source is being used?

This is a very important question since ion sources produce a very wide variety of results. A source such as an electron impact source will produce a lot of fragments and mostly odd electron species with one charge where a source such as an electrospray source will most commonly produce quasimolecular even electron species that can be multiply charged.

Is this an MS/MS spectrum?

Tandem mass spectrometry purposely produces fragment ions post source.

What is the origin of the sample?

By understanding the origin certain expectations can be assumed. For example, if the sample is coming out of a synthesis/manufacturing process impurities are likely to be present that are related to the major component. Another example would be if the sample is a relatively crude preparation of a biological sample the sample likely contains a certain amount of salt that may adduct to the analyte molecules in certain analyses.

How was the sample prepared? How was it run/introduced?

Samples often must be prepared for analysis. An important example would be which matrix was 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.

What are you trying to achieve?

This is the most overlooked basic question. To interpret data one must know the desired outcome (and have collected the right data in the first place). There are many bits of information that can be gleaned from mass spectrometry data. Examples would be 'what is the mass of my molecule?', 'how pure is my sample?, 'what is the structure of my molecule?' Each of these questions requires a different approach.

Applications

Isotope ratio MS

Mass spectrometry is also used to determine the isotopic composition of elements within a sample. Differences in mass among isotopes of an element are very small, and the less abundant isotopes of an element are typically very rare, so a very sensitive instrument is required. These instruments, sometimes referred to as isotope ratio mass spectrometers (IR-MS), usually use a single magnet to bend a beam of ionized particles towards a series of Faraday cups which convert particle impacts to electric current. A fast on-line analysis of deuterium content of water can be done using Flowing afterglow mass spectrometry, FA-MS. Probably the most sensitive and accurate mass spectrometer for this purpose is the accelerator mass spectrometer (AMS). 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. Labelling with stable isotopes is also used for protein quantitation (see below).

Exposure and burial dating

Exposure and burial dating techniques rely on the fact that an object under a few meters of overlying material, such as soil, sediment, rock, or ice, is shielded from cosmic radiation; however, when that object is moved to the surface of the Earth it is exposed to incoming radiation. While an object is exposed to this radiation, cosmogenic nuclides such as 10Be, 14C, 26Al, and 36Cl are produced. These elements are radioactive, and have a half-life of thousands to millions of years. Measurements are typically made using an accelerator mass spectrometer, which gives a ratio of stable to radio isotopes.

Exposure dating is a technique used to find an estimated time for which an object has been on the surface of the Earth. A mass spectrometer is able to measure the ratio of these radio-isotopes to that of the stable isotope, this ratio is then used to find the absolute amount of radio-isotope in the object. The absolute amount of radio-isotope is directly proportional to the time it has spent on the surface, making it possible to find the amount of time the object has been exposed once the rate of production for a radio-isotope is known.

Burial dating, another technique involving cosmogenic nuclides, estimates the length of burial of an object. For this technique the object is assumed to have been at the surface of the Earth for some time before it becomes buried. If the amount of time an object was at the surface prior to burial is known, an initial quantity of radio-isotopes may be assumed. All radio-isotopes decay in the same fashion and the half lives of all are known, which allows the two known chemical concentrations at two different times to be placed into equations that give the length of time the object was buried. Using the chemical composition of the sample, it is possible to find the amount of radio-isotope left in the object after burial.

Trace Gas Analysis

Several techniques use ions created in a dedicated ion source injected into a flow tube or a drift tube: selected ion flow tube (SIFT-MS), and proton transfer reaction (PTR-MS), are variants of chemical ionization dedicated for trace gas analysis of air, breath or liquid headspace using well defined reaction time allowing calculations of analyte concentrations from the known reaction kinetics without the need for internal standard or calibration.

Pharmacokinetics

Pharmacokinetics is often studied using mass spectrometry due to the complex nature of the matrix (often blood or urine) and the need for high sensitivity to observe low dose and long time point data. The most common instrumentation used in this application is LC-MS with a triple quadrupole mass spectrometer. 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 insuring 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 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 mass spectrometry for microdosing studies, which are seen as a promising alternative to animal experimentation.

Mass spectrometry of proteins

Mass spectrometry is an important emerging method for the characterization of proteins. The two primary methods for ionization of whole proteins are electrospray ionization (ESI) and matrix-assisted laser desorption ionization (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 analyser. In the second, proteins are enzymatically digested into smaller peptides using an agent such as trypsin or pepsin. Other proteolytic digest agents are also used. The collection of peptide products are then introduced to the mass analyser. This is often referred to as the "bottom-up" approach of protein analysis.

Whole protein mass analysis is primarily conducted using either time-of-flight (TOF) MS, or Fourier transform ion cyclotron resonance. These two types of instrument are preferable here because of their wide mass range, and in the case of FT-ICR, its high mass accuracy. Mass analysis of proteolytic peptides is a much more popular method of protein characterization, as cheaper instrument designs can be used for characterization. Additionally, sample preparation is easier once whole proteins have been digested into smaller peptide fragments. The most widely used instrument for peptide mass analysis is the quadrupole ion trap. Multiple stage quadrupole-time-of-flight and MALDI time-of-flight instruments also find use in this application.

Protein and peptide fractionation coupled with mass spectrometry

Proteins of interest to biological researchers are usually part of a very complex mixture of other proteins and molecules that co-exist in the biological medium. This presents two significant problems. First, the two ionization techniques used for large molecules only work well when the mixture contains roughly equal amounts of constituents, while in biological samples, different proteins tend to be present in widely differing amounts. If such a mixture is ionized using electrospray or MALDI, the more abundant species have a tendency to "drown" signals from less abundant ones. The second problem is that the mass spectrum from a complex mixture is very difficult to interpret due to the overwhelming number of mixture components. This is exacerbated by the fact that enzymatic digestion of a protein gives rise to a large number of peptide products.

To contend with this problem, two methods are widely used to fractionate proteins, or their peptide products from an enzymatic digestion. The first method fractionates whole proteins and is called two-dimensional gel electrophoresis. The second method, high performance liquid chromatography is used to fractionate peptides after enzymatic digestion. In some situations, it may be necessary to combine both of these techniques.

Gel spots identified on a 2D Gel are usually attributable to one protein. If the identity of the protein is desired, the gel spot can be excised, and digested proteolytically. The peptide masses resulting from the digestion can be determined by mass spectrometry using peptide mass fingerprinting. If this information does not allow unequivocal identification of the protein, its peptides can be subject to tandem mass spectrometry.

Characterization of protein mixtures using HPLC/MS is also called shotgun proteomics and mudpit. A peptide mixture that results from digestion of a protein mixture is fractionated by one or two steps of liquid chromatography. The eluent from the chromatography stage can be either directly introduced to the mass spectrometer through electrospray ionization, or laid down on a series of small spots for later mass analysis using MALDI.

Protein identification

There are two main ways MS is used to identify proteins. Peptide mass fingerprinting (mentioned in the previous section) uses the masses of proteolytic peptides as input to a search of a database of predicted masses that would arise from digestion of a list of known proteins. If a protein sequence in the reference list gives rise to a significant number of predicted masses that match the experimental values, there is some evidence that this protein was present in the original sample.

Tandem MS is becoming a more popular experimental method for identifying proteins. Collision-induced dissociation is used in mainstream applications to generate a set of fragments from a specific peptide ion. The fragmentation process primarily gives rise to cleavage products that break along peptide bonds. Because of this simplicity in fragmentation, it is possible to use the observed fragment masses to match with a database of predicted masses for one of many given peptide sequences. Tandem MS of whole protein ions has been investigated recently using electron capture dissociation and has demonstrated extensive sequence information in principle but is not in common practice. This is sometimes referred to as the "top-down" approach in that it involves starting with the whole mass and then pulling it apart rather than starting with pieces (proteolytic fragments) and piecing the protein back together using De novo repeat detection (bottom-up).

Protein quantitation

Several recent methods allow for the quantitation of proteins by mass spectrometry. Typically, stable (e.g. non-radioactive) heavier isotopes of carbon (C13) or nitrogen (N15) are incorporated into one sample while the other one is labelled with corresponding light isotopes (e.g. C12 and N14). The two samples are mixed before the analysis. Peptides derived from the different samples can be distinguished due to their mass difference. The ratio of their peak intensities corresponds to the relative abundance ratio of the peptides (and proteins). The most popular methods for isotope labelling are SILAC (stable isotope labelling with amino acids in cell culture), ICAT (isotope coded affinity tagging), ITRAQ (isotope tags for relative and absolute quantitation).

History

In 1886, Eugen Goldstein observed "rays" that traveled through the channels of a perforated cathode in a low pressure gas discharge and moved toward the anode, in the opposite direction to the negatively charged cathode rays. Goldstein called these positively charged anode rays "Kanalstrahalen" or canal rays. Wilhelm Wien 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 mass to charge ratio. Wien found that the mass to charge ratio depended on the nature of the gas in the discharge tube.

The first mass spectrography technique was described in an 1899 article by English scientist J.J. Thomson. The processes that more directly gave rise to the modern version were devised by Arthur Jeffrey Dempster and F.W. Aston in 1918 and 1919 respectively.

In 2002, the Nobel Prize in Chemistry was received by John Fenn for the development of electrospray ionization (ESI) and Koichi Tanaka for the development of soft laser desorption (SLD) in 1987. An improved SLD method, matrix-assisted laser desorption/ionization (MALDI), was developed by Franz Hillenkamp and Michael Karas in 1988. The choice of Tanaka to receive the Nobel Prize for this work over Hillenkamp and Karas is a contentious issue to some people in the field. The two methodologies are remarkably similar yet significantly different. The work of Hillenkamp and Karas is fundamentally the same as the current implementation of matrix-assisted laser desorption/ionization which is now ubiquitous in mass spectrometry. Hillenkamp and Karas also demonstrated exceptionally well the importance of this new technique. On the other hand the work of Tanaka is similar and published sufficiently earlier such that the work of Hillenkamp and Karas could in theory be a derivative improvement. Yet, the work of Tanaka on SLD may have never come to prominence or become particularly useful without further improvement. The choice of John Fenn to receive the Nobel Prize is not controversial, however electrospray processes had been studied for most of the twentieth century and the concept of ESI-MS was proposed nearly twenty years earlier by Malcolm Dole.

See also

• Electron spectrometer
• Blackbody infrared radiative dissociation
• Calutron
• Chemical ionization
• Collision-induced dissociation
• Electron capture dissociation
• Electron ionization
• Electron multiplier
• Electrospray ionization
• Faraday cup
• Fourier transform ion cyclotron resonance
• Gas chromatography-mass spectrometry
• Helium mass spectrometer
• ICP-MS
• Infrared multiphoton dissociation
• Ion source
• Liquid chromatography-mass spectrometry
• Mass spectrum
• Matrix-assisted laser desorption/ionization
• Microchannel plate detector
• Quadrupole ion trap
• Quadrupole mass analyzer
• SIFT-MS selected ion flow tube mass spectrometry
• Secondary ionisation
• Sector instrument
• Taylor cone
• Thermal ionisation
• Time-of-flight

External links

• American Society for Mass Spectrometry
• Australian and New Zealand Society for Mass Spectrometry
• British Mass Spectrometry Society
• Canadian Society for Mass Spectrometry
• International Mass Spectrometry Society
• A History of Mass Spectrometry (Scripps)
• Mass spectrometer simulation An interactive application simulating the console of a mass spectrometer
• Mass spectrometry terms wiki
• SILAC web resource Detailed information about the SILAC method

References

• McLafferty, F. W. and Turecek, F., Interpretation of Mass Spectra, University Science Books; 4th edition (May, 1993) ISBN 0935702253
• Tuniz, C., et al., "Accelerator Mass Spectrometry: Ultrasensitive Analysis for Global Science", CRC Press, (1998) ISBN 0849345383
• Muzikar, P., et al., "Accelerator Mass Spectrometry in Geologic Research", Geological Society of America Bulletin v. 115 (2003) p. 643 - 654.