simplified diagram of a mass spectrometer

Doc Brown's Chemistry

Appendix 4. MASS SPECTROMETER - MASS SPECTROSCOPY

Appendix 4a Introduction to the Mass Spectrometer - mass spectrometry

The mass spectrometer is an instrument by which you can separate ionised/charged (+) particles of different mass and determine the amounts of each particle in a mixture.

The technique is called mass spectroscopy or mass spectrometry ('mass-spec' and 'MS' in shorthand!). How can mass spectrometry be used to measure percentage isotopic composition of an element (isotopic abundance) and determine the relative atomic mass of an element? The examples feature the mass spectra of chlorine, bromine, ethanol and strontium and its relative atomic mass determination and calculation.

Some abbreviations used: A = mass number,    Ar = relative atomic mass,   Z = atomic number (NOT z)

m/z = relative molecular mass or isotopic mass / electric charge for ions formed in a mass spectrometer

Mass spectrometry gives accurate information on the relative masses of isotopes and their relative abundance (proportions).

Mass spectrometry is an important method of analysis in chemistry and can be used to identify elements and compounds by their characteristic mass spectrum pattern - the technique is used in planetary space probes e.g. mass spectrometer instrumentation is incorporated in the Mars explorer vehicles.


Mass Spectroscopy - an instrumental method of analysis

The instrument used is called a mass spectrometer, of which there are several types.

All types of mass spectrometers involve vapourising atoms or molecules in high vacuum and subjecting the vapourised particles to electron bombardment to generate a beam of positive ions, a process called ionisation.

The mass spectrometer, by several different means, separates and counts the numbers of different positive ion particles produced.

The resulting data from the detector is called a mass spectrum (plural mass spectra).


Method (1) DEFLECTION MASS SPECTROMETER

(NOTE: Most mass spectrometers these days are of the TOF type!, and students now, and in the future, should be expected know how a TOF works, the results are ultimately the same, but I've described the older type of mass spectrometer as an introduction to mass spectroscopy of the atoms and molecules of elements and compounds)

My use of the word 'deflection' in describing this type of mass spectrometer is NOT official, but I couldn't think of any other way of distinguishing it from a 'time of flight' mass spectrometer described in method (2) at the end of this page!

The relative paths of light to heavy ions in a mass spectrometer tubeThe substance to be analysed is introduced/injected into a high vacuum (extremely low pressure) tube system (at K left diagram) where the particles are ionised by colliding with beam of high speed electrons (at Q in left diagram).

Note: If the sample is not already a gas, then a liquid or solid substance must be vapourised, i.e. the material must be in the gaseous state to be analysed in a mass spectrometer. The material being analysed must in the form of free moving gaseous atoms or molecules which can be then bombarded with electrons to produce equally free moving positive ions which can rapidly be accelerated in a powerful electric field. It is the manipulation of the stream of gaseous ions that forms the basis of mass spectrometry.

You cannot analyse any liquid or solid material in this way unless it is vapourised.

The resulting (+) ions are accelerated down a tube (from + to - plates, P in left diagram) and then through a powerful magnetic field.

The charged or ionised particles are deflected by this powerful magnetic field (R in left diagram).

How much they are deflected depends on the particle mass and the speed of the particle and the strength of a magnetic field i.e. lighter particles of lower mass (and momentum) are deflected more than heavier particles of bigger mass (see right diagram below) for a given set of conditions.

By varying the strength of the magnetic field, it is possible to bring into focus onto an ion detector (N in left diagram) at the end of the tube (effectively an electrical event is detected), every possible mass in turn and a measure the strength of the ion current, which is a measure of how much of that ion has been formed from the sample under analysis.

A simplified diagram of a mass spectrometer tube system is shown below (left) with further explanation as to what is going on and an extra diagram to show the relative paths of light to heavy ions for a given strength of magnetic field.

simplified diagram of a mass spectrometer The relative paths of light to heavy ions in a mass spectrometer tube

KEY TO DIAGRAM and more detail of each component's function

K = sample injection point, it must be a gas, so a liquid/solid must be vaporised at the injection point.

IONISATION

Q = high voltage (high +/- p.d.) electron gun which fires a beam of high speed/energy electrons from a heated 'metal element' into the vaporised sample under analysis and causes ionization of the atoms (or molecules) forming positive ions (mainly monopositive in charge).

The collision of high KE electrons with atoms or molecules causes another electron to be knocked off the particle leaving a negative deficit i.e. a positively charged particle is formed e.g.

M(g) + e- ==> M+(g) + 2e-, usually written as just

M(g) ==> M+(g) + e- (M might represent e.g. a metal atom or a molecule)

The ions formed should be written as [M]+, a notation that is handy if you are dealing with ionised molecule fragments with an overall single positive charge e.g. [CH3]+ is seen in the mass spectrum of methane gas, CH4.

The low pressure (~vacuum) is needed to prevent the ions from colliding with air particles which would stop them reaching the ion detector system.

ACCELERATION

P = are negative plates which accelerate the positive ions down the tube (there are positive plates at the start of the tube). A moving beam of charged particles creates a magnetic field around itself, and this 'ion beam' magnetic field interacts with the magnetic field at R.

DEFLECTION-SEPARATION

R = the magnetic field that causes deflection of ions, this is can be varied to change the extent of deflection for a given mass and to focus a beam of ions of particular mass down onto the detector. Hence, by programming the mass spectrometer to 'sweep' through all likely particle masses, in terms of the right hand diagram, you can increase the strength of the magnetic field to bring into focus onto the ion detector monopositive ions of increasing mass.

DETECTION

N = an ion detection system which essentially generates a tiny electrical current when the ions hit it. The positive ions 'grab' an electron on the detector which is replaced in the detector circuit by another electron. This causes a minute electric current which can be amplified. The strengths of the 'electronic' signals from the various ion peaks are sent to a computer for analysis, computation and display. They tell you the particle masses present and their relative abundance (see the mass spectrum diagram for the element strontium below). The data is then presented as an m/z versus peak height.

m/z means the relative mass of the ion over its charge, which for our purposes the electric charge is +1 (lower case z) and the mass (lower case m) is the relative atomic/formula mass of the particle ionised. You should write the structure of the ion in square brackets and put the charge on the outside of them in the top right - this is an important and universally accepted notation in mass spectrometry.

Examples of m/z values (mass/charge ratio) m/z values apply to ALL methods of mass spectrometry (see TOF later)

ion relative mass (m) positive ion charge (z) m/z ratio
[14N]+ 14 1 14/1 = 1
[56Fe]+ 56 1 56/1 = 56
[56Fe]2+ 56 2 56/2 = 28
[35Cl]+ 37 1 35/1 = 35
[35Cl2]+ 70 1 70/1 = 70
[35Cl2]2+ 70 2 70/2 = 35
[CH3]+ 15 1 15/1 = 15

Note that you can get multiple charged ions, but most mass spectral analysis is based on mono-positive ions.

Other terms used: monatomic/mononuclear ions are derived from one atom (eg [35Cl]+ or [88Sr]+ and a molecular ion is derived from more than one atom (eg [Cl2]+ or [C6H5COOH]+).


MASS SPECTRUM

The resulting record of the ion peaks is called the mass spectrum or mass spectra. The highest peak is called the base peak and is often given the relative and arbitrary value of 100, particularly in the mass spectra of organic compounds.

MASS SPECTRA

For elements you get a series of signals or ion peaks for each isotope present and the ratio of peak heights gives you the relative proportion of each isotope in the element so that you can calculate the relative atomic mass of an element. This 'simple' spectra of mononuclear ions like [Sr]+ is only true for non-molecular elements like metals (see mass spectrum of strontium diagram below) or noble gases, but for molecular elements like nitrogen or the halogens things are not so simple (see chlorine example below).

The proportions or percentages of all the isotopes of an element is often called the isotopic abundance.

For larger e.g. organic molecules, things can be very complex indeed, as molecules fragment and many different ions can be formed BUT you can get the relative molecular mass of a molecule by identifying what is called the molecular ion peak, that is, when one electron is knocked of the molecule but the molecule retains its full molecular structure.

e.g. (c) doc bbenzoic acid (Mr = 122) gives a molecular ion peak of m/z = 122, due to [C6H5COOH]+

but you also get fragments such as [C6H5]+ with an m/z of 77 as the molecule breaks up on further electron impact.

m/z explained


CHLORINE EXAMPLE

The mass spectrum of chlorine is a good example of a molecular element whose mass spectra can be a bit tricky when first encountered.

Chlorine consists of two principal stable isotopes, chlorine-37 (~25% is 37Cl) and chlorine-35 (~75% is 35Cl).

Ar(Cl) is ~35.5 using the above percentages

from Ar(Cl) = [(75 x 35) + (25 x 37)] / 100

BUT, chlorine consists of Cl2 diatomic molecules, which may or may not split on ionisation, so how can we explain the presence of five peaks and not just two for the two isotopes?

The result of the ionisation process and subsequent fragmentation of chlorine molecules is a series of 5 different mass peaks from the various isotopic monatomic or molecular ion possibilities.

  1. [37Cl37Cl]+ or [37Cl2]+ m/z = 74  (molecular ion)

  2. [37Cl35Cl]+ m/z = 72 (note that you must show the two isotopes separately in the molecular ion)

  3. [35Cl35Cl]+ or [35Cl2]+ m/z = 70  (molecular ion)

  4. [37Cl]+ m/z = 37  (mononuclear ion, monatomic fragment)

  5. [35Cl]+ m/z =35  (mononuclear ion, monatomic fragment)

Reminder: (i) m/z means the relative mass of the ion over its charge (m/z explained), (ii) monatomic/mononuclear ions are derived from one atom, (iii) a molecular ion is derived from more than one atom.

So, the presence of five peaks is explained and the ratio of the peak heights can be explained by considering a simple probability table of all the permutations possible for the monatomic or molecular ions - remember in a mass spectrometer you are dealing with millions of 'randomised' particles.

m/z 35Cl 35Cl 35Cl 37Cl
35Cl 70 70 70 72
35Cl 70 70 70 72
35Cl 70 70 70 72
37Cl 72 72 72 74

The ratio of heights for peaks 1 and 2 is 3 : 1, the ratio of the isotopic abundance.

For the bimolecular ions, (left table of possibilities) we assume (for simplicity) that exactly 3/4 (75%) of the chlorine isotopes are 35Cl and 1/4 (25%) of the isotopes are 37Cl.

This gives an expected ratio of the molecular ions 70 : 72 : 74 of 9 : 6 : 1, and this is what you observe for peaks 3 to 5.

The ratio of the heights of the first set of peaks (1-2) to the heights of the 2nd set (3-5) depends on the energy and intensity of the ionising beam of electrons. The greater this is, the greater the fragmentation of the molecules i.e. peaks 1-2 would increase and peaks 3-5 would decrease relative to each other, BUT, the height ratios would stay the same in each set i.e. the monatomic/mononuclear ions and the diatomic molecular ions.

For identifying molecules from a fingerprint pattern you should operate the mass spectrometer under the same conditions i.e. standards and unknowns compared under the same operating conditions to give reproducible mass spectra.

Other examples and explanation of the calculation of the relative atomic mass of an element using % of isotopes is given in Part 1 of GCSE-AS (basic) calculations.

The simplest and best example on this page of calculating relative atomic mass from a mass spectrum is fully explained for the metallic element strontium.


STRONTIUM EXAMPLE using mass spectra data to calculate relative atomic mass

A 'simple' element mass spectrum to interpret AND a subsequent relative atomic mass calculation based on the mass spectroscopy of the element strontium

The mass spectrum of the element strontium

The relative atomic mass of an element, Ar, is the weighted average mass of the isotopes present, compared to 1/12th of the relative mass of the carbon-12 isotope. [ 12C is given the relative mass value of 12.0000 ]

Quite often the highest m/e peak is arbitrarily given the relative value of 100, as in this case and referred to as the base peak, but the peak lines might well indicate % abundance of isotopes. The diagram of abundances is sometimes called a stick diagram.

Relative peak height = relative abundance as measured from the ion current detector signal.

The mass spectrum shows strontium consists of four isotopes giving rise to four positive ions - relative peak heights of

84Sr (peak height = 0.68), 86Sr (peak height = 12.0),87Sr (peak height = 8.47) and 88Sr (peak height = 100.0)

The sum of the heights = 0.68 + 12.0 + 8.47 + 100.0 = 121.15

So we can now calculate the weighted average mass of ALL the isotopes.

Therefore Ar = {(0.68 x 84) + (12.0 x 86) + (8.47 x 87) + (100.0 x 88)}/121.15 =  87.7

The book value is 87.62, BUT this calculation does NOT take into account the very accurate relative atomic masses based on the carbon-12 scale, it merely uses the mass numbers, which are always integer.


Another relative mass calculation from mass spectrometry

Potassium has three naturally occurring isotopes, stable 39K and 41K, and the long-lived 40K (half-life of millions of years!)

The mass spectrum of potassium generated the following data:

m/z 39 40 41
relative % abundance 93.258 0.012 6.730

Calculate the relative atomic mass of potassium.

Ar(K) = average mass of all the potassium atoms present.

= {(39 x 93.258) + (40 x 0.012) + (41 x 6.730)} / 100

= {(3637.062) + (0.48) + (275.93)} / 100 = 3913.472 / 100 = 39.13 (4sf, 2dp)

More on relative atomic mass calculations


The mass spectrum of bromine Br2

You get five peaks in the spectra of bromine molecules. For molecules completely atomised you get two peaks (m/z) of almost equal height from [79Br]+ and [81Br]+ mononuclear ions.

Because its ~50% of each isotope, the relative atomic mass of bromine is ~80 and hence the equality of peaks 1 [79Br]+ and 2 [81Br]+ from the monatomic ions from the fragmentation and ionisation of bromine molecules.

However, as with chlorine, molecular bromine is also ionised without fragmentation, giving rise to three more ion permutations (3 more m/z peaks).

[79Br79Br]+ (158), [79Br81]Br+ (160) and [81Br81Br]+ (162)

So! the presence of all five peaks is explained in the mass spectrum of bromine, and, because you are dealing with millions of randomised ionised atoms, the ratio of the two monatomic peaks can be used to accurately determine the relative atomic mass of bromine.

The data book quotes for the stable isotopes: 79Br (50.69%) and 81Br (49.31)

The ratio of the heights for the monatomic ions in the mass spectrum of bromine would 50.69 : 49.31 ~ 1 : 1 as observed.

Ar(Br) = (50.69 x 79) + (49.31 x 81) / 100 = 79.90

m/z 79Br 81Br
79Br 158 160
81Br 160 162

The ratio of the 2nd set of peaks (3 to 5) can be readily explained with a simple probability table, and a bit simpler than the chlorine example!

This assumes (for simplicity) that we have exactly 50% bromine-79 and 50% bromine-81 isotopes and how they might be combined in the molecular ions on a random basis.

The ratio of peak heights expected for m/z values of 158 : 160 : 162 would be 1 : 2 : 1

 and this is what you observe in the mass spectrum of bromine.


The mass spectra of organic compounds can be very complex as the molecules fragment under electron bombardment, but the resulting mass spectra can used to identify compounds from their 'finger-print' pattern of ion peaks of different mass and particular proportions for a given set of experimental conditions.

The largest m/z value gives the molecular mass of a molecule, i.e. the ion of largest mass, prior to fragmentation, is formed when the original whole and neutral molecule, loses one electron e.g. for ethane it would be due to the formation of [C2H6]+, m/z = 30 and is called the molecular ion peak.

Above is the mass spectrum of ethanol where the maximum molecular ion peak has an m/z value of 46 (M),

i.e. [CH3CH2OH]+, and, because it is a singly charged positive ion, this must be equivalent to the whole molecule minus one electron.

This description does ignore the presence of molecular ion of one mass unit more due to some molecules having a carbon-13 isotope in them (M+1 molecular ion)

In a mass spectrometer the ions fragment giving a characteristic set of peaks that can be used to identify a compound. e.g. 15 corresponds to [CH3]+ and 31 corresponds to [CH2OH]+ etc.

think of possible fragmentations to give m/z values of 15 or 31 ...

[CH3CH2OH]+  ==>  [CH3]+ + [CH2OH]      or      [CH3CH2OH]+ ==> [CH3] + [CH2OH]+

The fragmentation pattern is unique and characteristic of a particular compound, hence mass spectrometry can be used as an identification test procedure.


ISOTOPIC MASSES - definition and uses

The relative isotopic mass of an isotope is the accurate mass based on the carbon-12 scale, Ar(12C) = 12.0000

Very accurate isotopic masses are usually a tiny fraction different from a whole number but provide invaluable information.

Modern mass spectrometers are exceedingly accurate and very sophisticated instruments and can measure mass to at least 4 decimal places. They can readily distinguish between N2, CO and C2H4 molecules, all with an integer Mr of 28.

The very accurate molecular ion masses are [N2]+ = 28.0061, [CO]+ = 27.9949 and [C2H4]+ = 28.0313

A very accurate mass spectrometer (for high resolution mass spectroscopy) can even differentiate between organic molecules of the same integer molecular mass.

e.g. for the molecular mass 103, some possible, however unlikely, molecular formulae could theoretically be

C5HN3 = 103.0170C3H5NO3 = 103.0269C2H5N3O2 = 103.0382C7H5N = 103.0427CH5N5O = 103.0494

BUT note: This data will NOT distinguish between structural isomers of the SAME molecular formula, but the fragmentation pattern will (see the ethanol mass spectrum diagram).


Calculations of % composition of isotopes

It is possible to do the reverse of a relative atomic mass calculation if you know the Ar and which isotopes are present.

It involves a little bit of arithmetical algebra.

The Ar of boron is 10.81 and consists of only two isotopes, boron-10 and boron-11

The relative atomic mass of boron was obtained accurately in the past and mass spectrometers can sort out the isotopes present.

If you let X = % of boron 10, then 100-X is equal to % of boron-11

Therefore Ar(B) = (X x 10) + [(100-X) x 11) / 100 = 10.81

so, 10X -11X +1100 =100 x 10.81

-X + 1100 = 1081, 1100 - 1081 = X (change sides change sign!)

therefore X = 19

so naturally occurring boron consists of 19% 10B and 81% 11B (the data books quote 18.7% and 81.3%)

It should be pointed out that the relative ratio of isotopes can be very accurately determined using a modern mass spectrometer AND individual isotopic masses can be measured to four decimal places - which were NOT used in the above calculation.


Method (2) TIME OF FLIGHT (TOF) MASS SPECTROMETER (the latest design in common use)

Appendix 4b How a Time of Flight Mass Spectrometer Works

Ion mass separation using a time-of-flight mass spectrometer - a more modern instrument

The principles of a simple time of flight (TOF) mass spectrometer involve ionisation, acceleration to give all ions constant kinetic energy, ion drift, ion detection and finally data analysis - all done by computers these days!

  • In a time-of-flight mass spectrometer the ions are formed in a similar manner by electron bombardment, and the resulting ions accelerated between electrically charged plates.

  • Again, the sample must be a gas or vapourised and is bombarded with an electron beam or laser beam to knock off electrons to produce positive ions - the singly charged ions are used for analysis.

  • However, the method of separation due to different m/e (m/z, mass/charge) values is then dependent on how long it takes the ion to travel in the drift region' i.e. in the drift region the particles are NOT under the influence of an accelerating electric field.

    • A time of fight mass spectrometer does NOT use a magnetic field to effect the separation of the positive ions.

  • So ...

    1. Once the sample is vaporised and bombarded with an electron beam, a beam of positive ions is produced

      • M(g) + e- ==> M+(g) + 2e-  (ionisation process, M can be an atom of a molecule)

    2. The ions are accelerated in the same way between positive to negative plates in an electric field of fixed strength i.e. constant potential difference.

    3. The particles are given a constant kinetic energy as they pass into the drift region.

    4. The ions are then collected and detected.

    5. The positive ions cause a tiny electrical effect in the detector which becomes the electronic signal to the computer which analyses and compares the strength of the signal for the different arrival times of the different masses.

  • The smaller the mass of the ionised particle (ionized atom, fragment or whole molecule) the shorter the time of flight in the drift region where no electric field operates.

  • This is because for a given accelerating potential difference, a lighter particle is accelerated more to a higher speed than a heavier ion, so the 'time of flight' down the tube is shorter.

  • Therefore the ions are distinguished by different flight times NOT by different masses being brought into focus with a magnetic field as described in section 4a BUT the separation by time of flight is still determined by the m/e (m/z) value of the ion.

  • The general principles of the separation are required knowledge but the mathematics is NOT needed by A level students, but if you are interested, a simplified summary is given below

    • t = Kinst√(m/q)

    • t = time of flight, m = mass of ion, q = charge on ion, = square root of

    • Kinst = a proportionality constant based on the instrument settings and characteristics e.g. the electric field strength, length of analysing tube etc.

    • Therefore t is proportional to the square root of the mass of the ion for particles carrying the same charge - the bigger the mass the longer the 'flight time'.

    • The first equation is derived partly from the extra mathematics outlined below.

    • KE = qV, the kinetic energy imparted to the ion is given by its charge x the potential difference of the accelerating electric field.

    • The acceleration, for a fixed electric field, results in an ion having the same kinetic energy (KE) as any other ion of the same charge q but the velocity v of the ion depends on the m/e (m/z) value.

    • v = d/t (or t = d/v), where v = velocity of accelerated particle in the drift region, d = length of tube in the drift region. (or t = d/v)

    • KE = 1/2mv2, so the bigger m, the smaller is v in the drift region and hence the basis of detecting ions of different mass by different 'flight times'.

    • The diagram makes the method look simple, but far from it, the instrument works in a pulsed manner i.e. pulsed electric field, and some pretty sophisticated electronics are used to analyse the signals from the detector and the software calculates the mass of the ion based on the drift flight time.

  • Ultimately the data for analysis and subsequent calculations is the same as that derived from a deflection mass spectrometer described in method (1).

  • Most mass modern mass spectrometers are of the 'time of flight' type.

    • They come in all sizes eg a small scale version was on board an orbiter called Cassini which was carried by the Cassini-Huygens mission spacecraft to investigate and analyse the upper atmosphere of Titan, one of Saturn's moons. A miniature mass spectrometer was also in the probe Huygens which actually landed on Titan. In both cases gases were identified from mass spectra data and the mass spectrometer was coupled with a gas chromatograph to provide more analytical data.

      •  Gases such as hydrogen, nitrogen, methane, argon, carbon dioxide were found in the upper atmosphere of Titan.

      • Near the surface of Titan, the gases detected included hydrogen, methane, nitrogen ,argon, carbon dioxide, C2N2 (interesting!) and other small organic molecules.

    • -


(c) doc b Basic GCSE/IGCSE/AS Atomic Structure Notes


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