# Mass spectrometry **Mass spectrometry** is the [[Analytical_chemistry|analytical]] technique that converts the molecules or atoms of a sample into [[Ion|ions]], sorts the ions by their mass-to-charge ratio *m/z*, and records how many arrive at each value; the result, a mass spectrum, is a bar chart of ion abundance against *m/z* from which the masses, formulas, structures and isotopic makeup of the components can be read.[^openstax-ch2] The technique began with J. J. Thomson's positive-ray apparatus of 1913, which split neon into two isotopes, and with Francis Aston's mass spectrograph of 1919, which earned him the 1922 Nobel Prize in Chemistry.[^thomson1913][^aston1919][^nobel1922] On the [[Chemistry]] flagship mass spectrometry opens Part XIII, *Practice*, under the heading *Analytical chemistry: mass spectrometry*, where the laws of Part XI are put to work; its spine neighbours are [[Isotope]], [[Chromatography]] and [[Inductively_coupled_plasma_mass_spectrometry|ICP-MS]], and the dense children [[Helium_mass_spectrometer]] and [[Gas_chromatography]] hang from it. In the microsim below the reader operates a magnetic-sector analyzer. Ions accelerated through a potential *V* enter a [[Magnetic_field|magnetic field]] *B* and are bent onto circles of radius `r = (1/B)·sqrt(2·m·V/q)`; the reader slides *B*, and each *m/z* in the beam lands on or off the detector slit. The preset beam is [[Chlorine|chlorine]], whose ³⁵Cl⁺ and ³⁷Cl⁺ ions arrive as a doublet in the ratio of about 3 : 1, and a readout computes the isotope-weighted atomic mass `M = Σ xᵢ·Mᵢ` from the peak heights. The curved paths are the instrument. ## History Thomson's *Rays of Positive Electricity and Their Application to Chemical Analyses* (1913) described the parabola spectrograph, in which positive rays deflected by parallel electric and magnetic fields traced a parabola for each *m/z* on a photographic plate; the plate for [[Neon|neon]] showed two parabolas, at masses 20 and 22, the first sign that a stable element has isotopes.[^thomson1913] Aston, Thomson's assistant, built a velocity-focusing mass spectrograph in 1919 that brought ions of one *m/z* to a sharp line regardless of speed, and found with it that isotope masses are nearly, but not exactly, whole numbers.[^aston1919][^nobel1922] Arthur Dempster built the first 180-degree magnetic sector with direction focusing and an electrical detector in 1918, the ancestor of the microsim's analyzer, and Alfred Nier's compact 60-degree sector of 1940 made isotope-ratio measurement routine and separated the isotopes of [[Uranium|uranium]] for the first [[Nuclear_fission|fission]] experiments on ²³⁵U.[^dempster1918][^nier1940][^nier1940b] The magnet-free analyzers followed: the quadrupole filter of Wolfgang Paul and Helmut Steinwedel in 1953, the time-of-flight design of William Wiley and Ian McLaren in 1955, and Fourier-transform ion cyclotron resonance from Melvin Comisarow and Alan Marshall in 1974.[^paul1953][^wiley1955][^comisarow1974] The soft ionization methods that opened the technique to proteins arrived in the late 1980s, electrospray from John Fenn's group and laser desorption from Koichi Tanaka and from Michael Karas and Franz Hillenkamp; Fenn and Tanaka shared the 2002 Nobel Prize in Chemistry.[^fenn1989][^karas1988][^tanaka1988][^nobel2002] ## Components A mass spectrometer consists of a sample inlet, an ion source, one or more mass analyzers, a detector and a data system, all but the last enclosed in a vacuum chamber pumped low enough that an ion crosses the instrument without a collision.[^averill-ch2] The source turns neutral sample into charged particles, usually by removing an [[Electron|electron]] or attaching a proton; the analyzer separates the ions in space or in time according to *m/z*; the detector converts each arriving ion into an electrical signal; and the data system assembles the spectrum. The choice of source and analyzer decides what can be measured, from the isotopes of a single [[Atom|atom]] to intact proteins of many thousand daltons, and the sections below take the parts in the order an ion meets them, from the inlet through the source and the analyzer to the detector and the spectrum that the data system finally records. ### Illustrative example Chlorine gas admitted to an electron-ionization source gives Cl⁺ and Cl₂⁺ ions. Because natural chlorine is 75.76 % ³⁵Cl and 24.24 % ³⁷Cl, the atomic ions appear at *m/z* 35 and 37 with heights in the ratio 3.13 : 1, and the molecular ions at 70, 72 and 74 in the ratio of about 9 : 6 : 1, since a [[Molecule|molecule]] of Cl₂ can carry two light atoms, one of each, or two heavy.[^meija2016b] Weighting the isotope masses by the two peak heights of the microsim's doublet, `M = 0.7576 × 34.969 + 0.2424 × 36.966 = 35.45 u` (derived), reproduces the standard [[Atomic_mass|atomic weight]] of chlorine to three figures.[^openstax-ch2][^meija2016a] ## Sample inlet The inlet delivers sample to the source at a controlled rate. Gases and volatile liquids are leaked in through a valve, solids are heated on a probe, solutions arrive through a capillary, and in the coupled instruments treated below the inlet is the outlet of a separation column, so that a mixture's components enter one after another.[^averill-ch2] The inlet is also where the pressure drops to the source vacuum. ## Ion source The source sets what the spectrum can show. Hard ionization deposits enough energy to break the molecule into fragments, whose pattern is a fingerprint of structure; soft ionization leaves the molecular ion intact, which is what the mass of a large, fragile molecule requires.[^openstax-ch2] Most sources make singly charged ions, so that *m/z* equals the mass in daltons; electrospray makes ions carrying many charges, which brings heavy molecules into the range of an ordinary analyzer. ### Electron ionization In electron ionization a beam of electrons, conventionally at 70 [[Electronvolt|eV]], strikes gas-phase molecules and knocks out an electron to give a radical cation, M⁺·, with enough surplus energy that much of it fragments.[^averill-ch2] The fragmentation is reproducible between instruments, so libraries of electron-ionization spectra identify compounds by pattern matching. ### Spray ionization Electrospray ionization pumps a solution through a needle held at several kilovolts; the spray of charged droplets evaporates in a stream of warm gas until the ions inside are released intact, carrying a ladder of charge states that can be deconvolved to the neutral mass.[^fenn1989] Fenn's 1989 paper weighed proteins of tens of kilodaltons this way.[^fenn1989] ### Desorption ionization In matrix-assisted laser desorption/ionization the sample is co-crystallized with a small ultraviolet-absorbing matrix and struck with a [[Laser|laser]] pulse; the matrix absorbs the energy and carries the analyte into the gas phase as singly charged ions, largely without fragmentation.[^karas1988][^tanaka1988] The pulsed source is usually paired with a time-of-flight analyzer. ### Inductively coupled plasma For elemental analysis the sample is sprayed into an argon [[Plasma_(physics)|plasma]] at several thousand kelvin, which atomizes and ionizes it completely; the atomic ions give the elemental and isotopic composition down to trace levels, as the [[Inductively_coupled_plasma_mass_spectrometry|ICP-MS]] page describes. ## Mass analyzer The analyzer is the part of the instrument the microsim is about. Every analyzer uses electric or magnetic fields to make an ion's trajectory or timing depend on *m/z*, and every one follows the same two equations of motion. ### Theory An ion of [[Electric_charge|charge]] *q* accelerated from rest through a potential *V* acquires [[Kinetic_energy|kinetic energy]] `q·V = (1/2)·m·v²`, so its speed is `v = sqrt(2·q·V/m)`.[^uphys-ch11] In a uniform magnetic field *B* perpendicular to its velocity it feels the [[Lorentz_force|Lorentz force]] `F = q·v·B`, always at right angles to the motion, and circles with `q·v·B = m·v²/r`, giving `r = m·v/(q·B)`.[^uphys-ch11] Eliminating the speed gives the sector equation the microsim computes, `r = (1/B)·sqrt(2·m·V/q)`: at fixed *V* and *B* the radius grows as the square root of *m/q*, and a scan of *B* brings each *m/z* in turn onto a fixed slit.[^uphys-ch11] The same equations give the time-of-flight analyzer its flight time, proportional to sqrt(m/q), and the ion cyclotron its angular frequency `ω = q·B/m`, which depends on *m/q* but not on speed.[^uphys-ch11] Doubling the accelerating voltage in the microsim therefore widens every radius by sqrt(2), and doubling the charge of an ion halves its *m/z* and moves it to the position of an ion of half the mass. ### Analyzer characteristics Analyzers are compared by mass range, by resolving power, the ratio of a mass to the smallest difference that can be told apart at it, by mass accuracy and by speed. Sectors and quadrupoles give unit resolution cheaply; time-of-flight and Fourier-transform instruments resolve ions of the same nominal mass. ### Sector In a magnetic-sector instrument the ions leave the source through a slit and cross the field of an electromagnet; the ion whose radius matches the instrument radius passes the exit slit to the detector, and the others strike the walls.[^uphys-ch11] For the microsim's chlorine preset, a singly charged ³⁵Cl⁺ ion (34.969 u) accelerated through 2,000 V and bent in a field of 0.500 T follows a radius of 7.62 cm, and ³⁷Cl⁺ follows 7.83 cm, a separation of 2.1 mm at the focal plane (derived; ILLUSTRATIVE geometry). Sliding *B* upward shrinks every radius by the same factor, so the light ion, whose radius is the smaller, is brought onto the slit first and the heavy ion follows as the field rises a further 2.8 %, the square root of 37/35; the detector trace against *B* is the spectrum. A double-focusing sector adds an [[Electric_field|electric]] sector that corrects for the spread in ion energies, which raised sector instruments to the resolving power needed for exact-mass work.[^averill-ch2] ### Time-of-flight A time-of-flight analyzer gives all ions the same kinetic energy with a pulsed field and lets them drift down a field-free tube; light ions arrive first, and the arrival time gives *m/z* through `t = L·sqrt(m/(2·q·V))`. Wiley and McLaren's 1955 design focused ions of different starting positions to the same arrival time; a reflectron, added later, corrects for the spread in initial energy, and every pulse yields a whole spectrum.[^wiley1955] ### Quadrupole mass filter Paul and Steinwedel's quadrupole uses four parallel rods carrying a radio-frequency voltage with a direct-voltage offset; for a given ratio of the two only ions in a narrow band of *m/z* follow stable paths down the axis.[^paul1953] Scanning the voltages scans the mass, and the device is cheap, compact and fast. ### Ion traps A quadrupole ion trap closes the same fields into a three-dimensional cell and ejects the stored ions in order of *m/z*; an orbitrap holds ions in orbit around a spindle electrode and reads their axial oscillation frequency, proportional to sqrt(z/m), by Fourier transform, reaching resolving powers well over a hundred thousand.[^makarov2000] ### Fourier-transform ion cyclotron resonance In a strong magnetic field trapped ions circulate at the [[Cyclotron|cyclotron]] frequency `ω = q·B/m`; a radio-frequency pulse excites them into coherent orbits, and a [[Fourier_analysis|Fourier transform]] of the image current they induce on the cell plates converts frequencies to masses. Comisarow and Marshall introduced the method in 1974, and it remains the highest-resolution form of mass analysis.[^comisarow1974] ### High resolution High resolving power turns a nominal mass into an exact one. Because nuclide masses are not integers, every elemental formula has its own exact mass, and a measurement good to a few parts per million distinguishes an ion containing an [[Oxygen|oxygen]] atom from one containing a CH₄ group of the same nominal mass.[^aston1919] ## Detectors The detector converts a stream of ions into a current. An electron multiplier, in which each ion striking a surface releases secondary electrons that cascade down a chain of dynodes, gives a gain of a million or more and counts single ions; a Faraday cup collects the ion charge directly where accuracy matters more than sensitivity, as in isotope-ratio work.[^averill-ch2] ## Tandem mass spectrometry Tandem mass spectrometry places two stages of analysis in series with a collision cell between them. The first analyzer selects one *m/z*, the ions are fragmented by collisions with an inert gas, and the second records the fragments; the pattern identifies the precursor and, for a peptide, reads its sequence from the ladder of fragment masses.[^fenn1989] ## Common mass spectrometer configurations and techniques Instruments are named by the sequence of their parts. A gas chromatograph feeding an electron-ionization source and a quadrupole is the workhorse of environmental and forensic work; laser desorption feeding a time-of-flight analyzer serves microbial identification; electrospray feeding a quadrupole–time-of-flight or an orbitrap serves proteins; an inductively coupled plasma feeding a quadrupole serves trace elements.[^averill-ch2] ## Separation techniques combined with mass spectrometry A mass spectrometer sees everything that enters the source at once, so mixtures are separated first and the spectrometer serves as the detector of the separation; liquid chromatography and capillary electrophoresis are coupled through electrospray, gas chromatography directly. ### Gas chromatography In [[Gas_chromatography|gas chromatography]]–mass spectrometry the components of a volatile mixture leave the column one at a time and are ionized as they arrive, so that each peak of the chromatogram carries its own spectrum and a component is identified by both retention time and fragmentation pattern.[^averill-ch2] ## Data and analysis The output of an instrument is a list of *m/z* values and intensities, and the analysis turns that list into chemistry. Two steps are involved: drawing the list as a spectrum, and reading formulas, structures and abundances out of the peaks. ### Data representations A mass spectrum is drawn as vertical lines at each *m/z* with heights proportional to abundance, normalized so that the tallest line, the base peak, is 100 %. The molecular ion, if it survives, is the highest-mass major peak, and the isotope peaks above it record the heavier isotopes of carbon, chlorine, bromine and sulfur.[^openstax-ch2] ### Data analysis Isotope patterns are the first thing an analyst reads. The isotope-weighted mass of an element is the abundance-weighted sum of its isotope masses, `M = Σ xᵢ·Mᵢ`; the Portal Book *Introductory Chemistry* works the case of [[Boron|boron]], 20 % ¹⁰B and 80 % ¹¹B, which gives 10.8 u, and the same arithmetic run in reverse on a spectrum gives the abundances from the peak heights.[^ball-119-120] The chlorine doublet of the microsim is that reversal: two peaks, one ratio, one average mass, and the [[Periodic_table|periodic table]]'s entry for chlorine is the answer it should return. For a molecule the pattern multiplies out: one chlorine gives peaks at M and M + 2 in the ratio 3 : 1, two chlorines give M, M + 2 and M + 4 in the ratio 9 : 6 : 1, and a single bromine gives a 1 : 1 pair. Exact masses and isotope patterns narrow the possible formulas of an unknown, fragment patterns narrow the structure, and library matching confirms it. ## Applications The technique reaches from the isotopic composition of rocks to the sequence of proteins; three applications are treated here, each using a different part of the instrument. ### Isotope ratio mass spectrometry Isotope-ratio instruments measure small differences in the ratios of stable [[Isotope|isotopes]], such as ¹³C/¹²C in [[Carbon|carbon]] and ¹⁸O/¹⁶O in oxygen, with the Faraday-cup sector design that Nier established, and report them as deviations from a standard in parts per thousand.[^nier1947] The ratios record temperature, diet and source; [[Radiocarbon_dating|radiocarbon dating]] by accelerator mass spectrometry counts ¹⁴C atoms directly. ### Protein characterization Electrospray and laser desorption made intact proteins measurable, and tandem mass spectrometry of their peptides reads sequences and locates modifications; the field of proteomics is built on these instruments, and the 2002 Nobel citation named soft ionization methods for the mass spectrometric analysis of biological macromolecules as the achievement.[^fenn1989][^nobel2002] ### Space exploration Mass spectrometers have flown on planetary missions since the Viking landers searched the Martian surface for organic compounds in 1976; the Sample Analysis at [[Mars]] suite on the Curiosity rover carries a quadrupole spectrometer coupled to a gas chromatograph.[^biemann1977][^mahaffy2012] ## See also - [[Isotope]] - [[Inductively_coupled_plasma_mass_spectrometry]] - [[Chromatography]] - [[Analytical_chemistry]] - [[Helium_mass_spectrometer]] - [[Gas_chromatography]] - [[Lorentz_force]] - [[Cyclotron]] ## References [^openstax-ch2]: Flowers, P.; Neth, E.; Robinson, W.; et al. (2019). *Chemistry: Atoms First*, 2nd ed. OpenStax. Chapter 2, "Atoms, Molecules, and Ions", pp. 73–114 (mass spectrometry; average atomic mass; the chlorine isotope example; page to pin). https://open.umn.edu/opentextbooks/textbooks/chemistry-atoms-first [^averill-ch2]: Averill, B.; Eldredge, P. (2011). *General Chemistry: Principles, Patterns, and Applications*. Index chapter 2, pp. 48–131 (mass spectrometry and the mass spectrometer; page to pin). https://open.umn.edu/opentextbooks/textbooks/general-chemistry-principles-patterns-and-applications [^ball-119-120]: Ball, D. W. (2011). *Introductory Chemistry*. Chapter 3, §3.3 "Masses of Atoms and Molecules", pp. 119–120 (isotope-weighted atomic mass; boron 20/80 → 10.8 u). https://open.umn.edu/opentextbooks/textbooks/introductory-chemistry [^uphys-ch11]: Sanny, J.; Ling, S. (2016). *University Physics Volume 2*. OpenStax. Chapter 11, "Magnetic Forces and Fields", pp. 475–512 (force on a moving charge; circular motion in a magnetic field; the mass spectrometer application; page to pin). https://open.umn.edu/opentextbooks/textbooks/university-physics-volume-2 [^meija2016a]: Meija, J.; et al. (2016). "Atomic weights of the elements 2013 (IUPAC Technical Report)." *Pure and Applied Chemistry* 88 (3): 265–291. https://doi.org/10.1515/pac-2015-0305 [^meija2016b]: Meija, J.; et al. (2016). "Isotopic compositions of the elements 2013 (IUPAC Technical Report)." *Pure and Applied Chemistry* 88 (3): 293–306. https://doi.org/10.1515/pac-2015-0503 [^thomson1913]: Thomson, J. J. (1913). *Rays of Positive Electricity and Their Application to Chemical Analyses*. London: Longmans, Green. [^aston1919]: Aston, F. W. (1919). "A positive ray spectrograph." *Philosophical Magazine*, 6th series, vol. 38. [^nobel1922]: The Nobel Prize in Chemistry 1922 (Francis W. Aston). NobelPrize.org. https://www.nobelprize.org/prizes/chemistry/1922/summary/ [^dempster1918]: Dempster, A. J. (1918). "A new method of positive ray analysis." *Physical Review*, vol. 11. [^nier1940]: Nier, A. O. (1940). "A mass spectrometer for routine isotope abundance measurements." *Review of Scientific Instruments*, vol. 11. [^nier1940b]: Nier, A. O.; Booth, E. T.; Dunning, J. R.; Grosse, A. V. (1940). "Nuclear fission of separated uranium isotopes." *Physical Review*, vol. 57. [^nier1947]: Nier, A. O. (1947). "A mass spectrometer for isotope and gas analysis." *Review of Scientific Instruments*, vol. 18. [^paul1953]: Paul, W.; Steinwedel, H. (1953). "Ein neues Massenspektrometer ohne Magnetfeld." *Zeitschrift für Naturforschung A*, vol. 8. [^wiley1955]: Wiley, W. C.; McLaren, I. H. (1955). "Time-of-flight mass spectrometer with improved resolution." *Review of Scientific Instruments*, vol. 26. [^comisarow1974]: Comisarow, M. B.; Marshall, A. G. (1974). "Fourier transform ion cyclotron resonance spectroscopy." *Chemical Physics Letters*, vol. 25. [^makarov2000]: Makarov, A. (2000). "Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis." *Analytical Chemistry*, vol. 72. [^fenn1989]: Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. (1989). "Electrospray ionization for mass spectrometry of large biomolecules." *Science*, vol. 246. [^karas1988]: Karas, M.; Hillenkamp, F. (1988). "Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons." *Analytical Chemistry*, vol. 60. [^tanaka1988]: Tanaka, K.; Waki, H.; Ido, Y.; Akita, S.; Yoshida, Y.; Yoshida, T. (1988). "Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry." *Rapid Communications in Mass Spectrometry*, vol. 2. [^nobel2002]: The Nobel Prize in Chemistry 2002 (John B. Fenn, Koichi Tanaka and Kurt Wüthrich). NobelPrize.org. https://www.nobelprize.org/prizes/chemistry/2002/summary/ [^biemann1977]: Biemann, K.; et al. (1977). "The search for organic substances and inorganic volatile compounds in the surface of Mars." *Journal of Geophysical Research*, vol. 82. [^mahaffy2012]: Mahaffy, P. R.; et al. (2012). "The Sample Analysis at Mars investigation and instrument suite." *Space Science Reviews*, vol. 170. ## Bibliography - Flowers, Neth, Robinson et al., *Chemistry: Atoms First*, 2nd ed. (OpenStax, 2019) — Portal Book 051, Chapter 2. - Averill and Eldredge, *General Chemistry* (2011) — Portal Book 050, index chapter 2. - Ball, *Introductory Chemistry* (2011) — Portal Book 056, §3.3. ## External links - [NIST Chemistry WebBook](https://webbook.nist.gov/chemistry/), reference electron-ionization mass spectra - [Open Textbook Library record for *University Physics Volume 2*](https://open.umn.edu/opentextbooks/textbooks/university-physics-volume-2) - The Wikipedia pair's external links list the rest. <!-- MATTERSIM:BEGIN g24 — Matter & Energy Cluster microsim (framework build, specs/sims/Mass_spectrometry.json); do not hand-edit inside --> **Microsim — three.js (Wikitube framework), pending deploy:** *Mass spectrometry* will play here once `https://wikitube-3d-microsims.netlify.app/matter/Mass_spectrometry.html` is live. <!-- pending: <div class="wt-sim" data-src="https://wikitube-3d-microsims.netlify.app/matter/Mass_spectrometry.html" data-title="Mass spectrometry"></div> --> <!-- MATTERSIM:END --> ## Wikipedia : Wikitube **Strict pair:** [Wikipedia](https://en.wikipedia.org/wiki/Mass_spectrometry) : [Wikitube](https://en.wikitube.io/wiki/Mass_spectrometry) · pinned revision [1369832347](https://en.wikipedia.org/w/index.php?oldid=1369832347) · 2026-09-11 ## Previous hub tags Hubs: `Life_Physics`. 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