What are the characteristics of mass spectroscopy

Mass Spectrometry Lexicon

α-cleavage - This homolytic bond cleavage is caused by the radical cation on a heteroatom. The functional groups can be ranked according to their α-cleavage activity.


Allyl cleavage - Homolytic fragmentation of an allyl bond. The driving force behind this cleavage is the formation of a stabilized cation. It is related to benzylic cleavage.

amu - atomic mass unit, is an outdated relative mass specification of atomic weights, which is based on the 16th part of the mass of the 16O isotope as a unit. It is often still used in discussions, usually as a rounded whole-number mass specification. See also Dalton (Da).

resolution - resolution - Ability of a mass spectrometer to separate ions with different m / z ratios, an important performance feature of an analyzer. There are different definitions:

  • 10% valley definition. If two peaks of equal intensity are separated so that the valley between the peaks is 10% of the peak height, then the resolution is R = m / Δm. With sector field devices this is the same over the entire mass range, with other analyzers the mass at which the ratio was determined must still be specified
  • 50% valley definition. Corresponds to the 10% valley definition.
  • Peak width definition m / Δm. For a singly charged peak, the ratio of mass to peak width is calculated. It must be stated at which height of the peak the width was measured. 10%, 5% are common (this results in the same numerical value as the 10% valley definition). It is also common to measure the width at half the peak height, abbreviated to FWHM (full width half mass).


Base peak - This ion is the most common ion in the considered mass range and is the standardization basis and is set = 100%. Caution, it is of course not possible to standardize on ions that are not also measured, so always include the mass range! Measurements for the interpretation of the spectrum should contain at least the masses from m / z 38.

Benzylic cleavage - Homolytic cleavage of a bond with the formation of a cation stabilized by an aromatic system. The term is also used when the aromatic ring is not a phenyl ring.

Bieman's law of displacement - If a chemical change is made to a molecule which is accompanied by a change in mass and which has no influence on the mass spectrometric fragmentation, then all fragments that contain this new structural element are shifted by this mass difference. Trivial facts are often difficult to formulate. This principle helps a lot in the interpretation of the spectrum. Optimal fragmentation-neutral markers are 2Dog 13C.

Dalton (Da) - Relative unit of mass, based on the 12th part of the mass of the 12C isotope. The official abbreviation is u.Mu or mmu is also used for the 1/1000 part of this mass.

Double bond equivalent (DBÄ, DBE) - A compound has the maximum number of hydrogen when: HMax = (Number of C atoms) x 2 + (number of N atoms) + 2. If you divide the difference to the number of H atoms found by 2, you get the number of DBA. A DBÄ means a double bond (also C-heteroatom) or a ring. In the presence of nitrogen, the rule must be modified.

Double bond problem - The position and the e / z isomerism of disubstituted double bonds cannot be determined directly under mass spectrometric conditions. The position of a double bond is usually determined by preparing suitable derivatives. Example: 9,10-bis (methylthio) octanoic acid methyl ester.

Doubly charged ions - The mass separation in the mass spectrometer takes place according to the mass / charge ratio, see d. doubly charged ions appear on half the mass. These ions can make interpretation more difficult if the mass spectrometer / EDP system only supplies whole-numbered masses. One then looks for a non-existent molecular symmetry. Doubly charged ions are to be expected in molecules with extended π systems. Example: 2,6-di-tert-butyl-p-cresol, biphenyl.

Unit resolution - This is the resolution at which neighboring masses are just sufficiently separated. Below sufficient is either 50% or 10% valley height. Of course, this must also be stated when comparing.

Electrospray Ionization (ESI) - Very gentle process for the production of ions introduced by Fenn. The solution of the substance is sprayed into an electric field. The separation into single molecules (or groups of molecules) takes place during the dissolution process. If ions arise spontaneously in solution, they can be detected directly, otherwise they only arise during the spraying process. This method offers the possibility of detecting non-covalently bound molecular assemblies.

Exact mass determination - Determination of the mass of an ion with an accuracy of ± 5 mmu. It is used to determine the elemental composition of an ion, because the alternative compositions often differ sufficiently in terms of their exact mass. The misnomer "high resolution" is often used for this.

Almost atom bombardment FAB - Ionization method in which the substance is mixed with a liquid matrix (glycerine, thioglycerine ...). Bombardment with fast neutral atoms triggers collision cascades that lead to the desorption of ions. It is widely used in peptide chemistry because this process results in structure-specific fragments. It is partly through ESI (with ==> MSn) replaced. The same result can also be achieved through bombardment with fast ions "liquid SIMS" ==> secondary ion mass spectrometry.

Field desorption (FD) - field desorption - very gentle ionization process in which the substance is applied to a very thin tungsten thread covered with needle-shaped carbon tips (produced by pyrolysis of benzonitrile). It has been largely superseded by ==> MALDI, ==> FAB and ==> ESI. It is still used in the investigation of apolar sensitive connections.

FWHM - ==> resolution

High resolution - Setting a resolution (m / Δm) of> 5000 for the separation of ions of the same nominal but different (real) mass. This term is often confused with exact mass determination.

Ion clusters - Group of mass lines belonging together due to the isotopic composition. The intensity ratios can be calculated by linear combination of the individual contributions.

Ion trap mass spectrometer (Iontrap)

  • Spherical ion trap. In a rotationally symmetrical structure consisting of a ring and two caps protruding into its opening, a volume is created in which ions can be stored using an alternating electric field. By varying the field, ions can be eliminated from the ion trap in a targeted manner (depending on their m / z ratio). These ions are detected with a detector. By using ion selection and excitation, multistage MS / MS experiments can be carried out in an ion trap MS.
  • Linear ion trap. Here the ions are trapped in a quadrupole rod system by applying blocking potentials to their ends. As with the spherical trap, the mass analysis is carried out by means of an instability scan. Linear traps are often used to condition packets of ions for subsequent analysis in the ICR or ==> Orbitrap trap.

FT-ICR - ==> Ion cyclotron resonance analyzer

Ion cyclotron resonance mass spectrometer - ICR mass analyzer in which ions are excited by an electrical pulse in a homogeneous magnetic field. The frequency of the resulting circular orbits is i.a. depends on the m / z ratio. These moving particles cause changing image voltages in a receiver. By analyzing the frequency mixture, the composition of the ion cloud can be calculated. Advantages:

  • no gap and multiplex advantage because the same ion cloud can be used multiple times to improve resolution and / or sensitivity.
  • With this type of MS, resolutions of> 106 reached!

Ionization energy - That is the energy to produce ions from the neutral molecules. For the radical cations formed under electron impact conditions, this is 6 -11 eV.

Ion series - Sequence of ions that differ by a constant amount of mass. They do not necessarily follow the same path of degradation.

Isolated charge concept - In order to rationalize mass spectrometric fragmentation paths, for the sake of simplicity one starts from the (false) assumption that the charge is concentrated at one location on the molecule.

Cargo competition - When a charged particle decays, both fragments compete for the positive charge. As a rule, it remains predominantly on the part with the lower ionization potential.

Laser desorption / ionization (LDI) - Evaporation and ionization with the help of a short laser pulse. The necessary irradiance is> 5 MW / cm2. Mostly in connection with a joint time mass spectrometer.

LDI - ==> laser desorption / ionization

"low voltage spectrum" - Formerly a widespread technique to reduce the excess energy of ions by ionization with 10-15 eV electron energy instead of the usual 70-80 eV - mostly for the purpose of relatively enlarging the molecular ion or to clarify fragmentation pathways (primary fragments become more intense). The use of "soft" ionization methods, e.g. chemical ionization, is preferred today.

m / z - The three-character symbol m / z is used around the dimensionless size to designate, which is divided by dividing the ion mass by the unified atomic mass unit (u) and through his Charge number (regardless of the sign) results. The symbol m / z is written in italics.

Matrix assisted laser desorption / ionization (MALDI or MALD) - Evaporation and ionization with a short laser pulse using a matrix substance (example: 2,5 dihydroxybenzoic acid). This takes on several tasks: separation of the substance molecules, absorption of the laser energy, joint sublimation with the substance, often protonating properties. With this method, very high molecular weight compounds can be investigated.

Mass-dependent rounding - Most organic compounds have a large number of hydrogen atoms. At 1.007 amu, these have a mass that is considerably higher than the integer. In order to take account of the increase in the decimal place and to be able to work with nominal dimensions as much as possible, a flexible rounding limit is set, which increases, for example, by 0.1 mass per 100 amu. In the case of low-hydrogen molecules, e.g. polyhalogenated compounds, which have a decreasing number of decimal places, this procedure leads to incorrect mass assignments.

McLafferty rearrangement - This rearrangement has a photochemical equivalent in the Norrish Type II rearrangement and other wet chemical counterparts, e.g. ester pyrolysis. It can be expected from a large number of compounds with double bonds. In the case of olefins with a disubstituted double bond, however, the double bond isomerization is faster (example: methyl stearate).

McLafferty +13 (+27, +41 ...) - Ion series that begins with an unspecific rearrangement of a hydrogen atom from the C6-C10 region to the charge center. Then an H atom is transferred back from the vicinity of the charge center (in the case of the McLafferty +13 from the α position). This is followed by a bond cleavage activated by the radical site (example: methyl stearate).

MS-MS coupling - Collective term for the combination of two (or) more mass analyzes. There is the interconnection of several analyzers (e.g. linear quadrupoles) (MS-MS "in space" "in space") but also multiple analysis one after the other in the same analyzer (MS-MS "in time" "in time"). The latter usually takes place in ion trap systems. Impact experiments are usually inserted between the mass analyzes.

Mother ion - ==> precursor ion

Loss of neutral particles - The formation of small stable neutral parts is often the driving force for fragmentation. The great formative energy of parts like H2O, HCN, CO, CO2, CM3SiF, SO2 etc. also makes otherwise unfavorable fragmentations possible.

Nominal mass - This is the addition of the rounded nuclide masses. From a mass of 500 or more, the rounded real mass can deviate from the nominal mass.

"Odd Electron Rule" - This rule states that a radical can only be lost once on a degradation path. The reason is to be seen in the limited amount of energy that an ion (see excess energy) has available for fragmentation. After an energy-intensive elimination of radicals, it is usually only sufficient to split off neutral particles (directly or after rearrangement). Violations of this rule often occur with compounds that split off particularly low-energy radicals (example: compounds with several iodine ligands), or when absolutely no other degradation pathways are available (example: methyl aromatics with several methyl groups).

Onium cleavage - This fragmentation is a frequent follow-up reaction to an α-cleavage at a heteroatom. The onium ion thus formed releases substituents as olefins with rearrangement of a hydrogen atom.

Orbitrap - Ion packets oscillate in a specially shaped chamber above a center electrode. Storage does not require a magnetic field. The mass analysis is done by measuring the pendulum speed of these parcels. The evaluation requires a Fourier transformation of the signal (very high resolution of 105 and exact mass determination possible).

Ortho effect - The spatial proximity of ortho substituents often opens up fragmentation paths that are not possible for the meta and para connection. They are often distinguishable from the latter, o- and m-isomers often have identical mass spectra.

production - product ion. Ion created by decay. Mostly in connection with the study of metastable fragmentation.

Quadrupole mass spectrometer - Symmetrical arrangement of 4 bars, of which the opposite ones are electrically connected. An alternating electrical voltage is applied to these pairs of rods. Ions that are introduced lengthways between the rods fly with a tumbling motion around the central axis. The alternating voltage can be chosen so that only the ions with an m / z ratio pass the rod system completely. The quadrupole MS acts like a mass filter.

Radical cleavage - In the simplest case, these decays only require the cleavage of a single bond, so they are fast, but energetically more complex than rearrangements (see "odd electron rule").

Space charge effect - Change in the spectrum due to the influence of an excessive space charge, e.g. in the case of IonTrap mass spectrometers. The AGC (Automatic Gain Control = shortening of the ionization time with increasing amount of substance) usually used there can only delay the use of this effect. This effect produces a "trail" in front of the peaks.

Real mass - (a bit outdated) This is the mass of a molecule that results from the combination of the masses of the pure nuclides. The deviation from the integer of the pure nuclide masses corresponds to the packing fraction (energy release during nuclear synthesis). The real mass is the mass spectrometrically relevant if the resolution of individual masses (or better) is given. It is measured when determining the exact mass of monoisotopic peaks.

Retro Diels-Alder reaction - A frequent degradation reaction if the corresponding structural requirements are met. The mass spectrometric variant does not necessarily have to run synchronously.

Secondary electron multiplier SEV - secondary ion multiplier SEM - detector for moving particles (photons, ions, neutral particles). These hit a conversion dynode and release electrons there. The electrons are accelerated in an electric field and generate (more) electrons when they hit a surface. This process is repeated like a cascade. The gain factors are between 104 and 107, detection of individual primary particles is possible. It is the most widely used detector in mass spectrometry.

"Self CI" (unwanted) chemical ionization of a substance with itself - In the case of an ion trap, this effect can usually be seen in the form of an M + 1 that is too strong. This signal then does not only consist of the 13C peak, but also from the (M + H)+generated by proton transfer to a neutral particle. The spectrum is therefore the superposition of an EI and CI spectrum. The discussion of fragmentation has to start with the (possibly invisible radical cation) M+ because the pseudomolecular ion as the product of a "soft" ionization shows little tendency to decay.

Key ion - A fragment that is typical for a certain structural feature e.g.m / z 74 for methyl ester. Attention, most of the rules of mass spectrometry have numerous exceptions!

Sector field mass spectrometer - sector field mass spectrometer - mass analyzer with one (or more) magnetic and possibly electric field (s). The ion beam entering the analyzer through an entrance slit is directed through an exit slit onto a detector after mass selection, focusing according to pulse and energy. The spectrum is created by varying the magnetic field. With special field geometries (e.g. Herzog-Matthauch geometry), an exit gap can be dispensed with, in which case a detector with spatial resolution is used (e.g. a photo plate).

Secondary ion mass spectrometry SIMS - secondary ion mass spectrometry - ionization process in which secondary ions are released from a surface with the help of a beam of fast ions (a few keV). This can be done with a high spatial resolution, s.d. a map of the surface can be obtained. Great importance in surface and semiconductor physics.

Silyl migration - The silyl group is a very rearrangement-friendly group. In some ways it behaves like a hydrogen atom (in wet chemistry it is called "proton equivalent"). Particularly noteworthy is the affinity for oxygen and halogens.

Spectrum tilt - GC / MS couplings with sector field devices and linear quadrupoles have the problem of the variable amount of substance during the measurement period of a spectrum. That is the reason why either the end of the spectrum or the beginning of the spectrum are overemphasized (scan on the rising or falling edge). This must be taken into account when comparing the spectra. IonTraps do not have this problem because the ions are temporarily stored.

Stoichiometric mass - This is the molecular weight determined from the elemental masses, which are based on the natural isotope ratio. In terms of mass spectrometry, it corresponds to the weighted mean value of the molecular ion cluster.

Thermal decays - It is often difficult to differentiate between mass spectrometric and thermal decays. In the case of the GC inlet, the usually shorter retention time of the pyrolysis products helps to identify them. In case of doubt, the inlet via a fast-heating thread (DCI or DEI) on a push rod is the best method to let thermally endangered connections into the MS.

Total ion current - In GC / MS, the GC trace is usually obtained from the spectrum data by adding up all the ion intensities of a scan (RIC = reconstructed ion chromatogram, II = integrated intensity). The rasterization in the scan cycle rhythm means a loss of resolution compared to the normal GC detector.

Daughter ion ==> production

u - atomic mass unit, which is 1/12 of the mass of the carbon isotope 12C refers.
(1u = m (12C) / 12 [kg]).

Excess energy - In the case of electron impact ionization, 2 -10 eV energy is transferred to the ion in addition to the ionization energy. This leads to an electronic and vibration excitation. The excess energy leads to fragmentation. The time available for this is 10 in the case of sector field devices-8s, with linear quadrupole MS approx. 10-7s and for IonTraps 10-3s.The duration of a molecular oscillation is approx. 10-12s, s.d. there is enough time for a redistribution of the vibrational energy.

Rearrangement - The fragmentation with rearrangement, in the simplest case this is a hydrogen shift, are energetically favorable reactions. But because the molecule has to adopt a certain geometry (entropy), they are slow processes. They often follow (rapid) homolytic bond cleavages. Rearrangements can take place over very large distances ("long range rearrangement"). One example is the formation of the m / z 147 from bis-trimethylsilyl compounds, which also takes place via chains of 40 carbon atoms!

Precursor ion - formerly “mother ion”, self-explanatory term for the investigation of metastable decays, that is decays that an ion suffers after leaving the ion source either spontaneously or through impact activation.