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Advanced Organic Chemistry: 15.1.2 Applications of Mass spectroscopy - Uses

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15.1.2 Uses of Mass spectrometry - Uses and applications of mass spectroscopy in analysis, investigating molecular structure and identification of compounds

Doc Brown's Chemistry Advanced Level Pre-University Chemistry Revision Study Notes for UK IB KS5 A/AS GCE advanced A level organic chemistry students US K12 grade 11 grade 12 organic chemistry courses involving molecular spectroscopy analysing mass spectra

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15.1.1 Theory of mass spectroscopy and how a mass spectrometer works

15.1.3 Index of mass spectra of organic compounds


Sub-index for this page

(a) Application of isotopic analysis

(b) Advantages of using mass spectrometry as an analytical technique

(c) Indentifying a molecule from the molecular ion peak and fragmentation pattern

(d) Analysis and identification using gas chromatography linked with mass spectrometry



(a) Applications of isotopic analysis (these sections open up in a new window for convenience)

(i) Analysing the ratio of isotopes of an element

You can measure very accurate masses of specific isotopes to at least 9 significant figures with high resolution mass spectrometers.

You can measure the relative abundances of the isotopes for a specific element - from this you can calculate the relative atomic mass of an element to at least 9 significant figures (which can also be measured from chemical analysis).

Simple examples are described and explained via the three links below.

The mass spectrum of chlorine - isotope peak ratios - calculating relative atomic mass

The mass spectrum of strontium - isotope peak ratios - calculating relative atomic mass

Analysing the mass spectrum of bromine - isotope peak ratios

(ii) Radiocarbon dating in archaeology

Archaeological dating of material using the isotope carbon-14 residue

(iii) Dating rocks

Geological dating of igneous rocks by measuring isotope ratios


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(b) Advantages of using mass spectrometry as an analytical technique

Like other modern instrumental analytical techniques used in chemistry in the 20th-21st centuries, mass spectroscopy has several advantages over traditional methods of chemical analysis e.g.

It is a very sensitive technique, only requiring tiny amounts of material for analysis and only tiny amounts might be available e.g. in forensic analysis of a crime scheme, drug analysis.

It is a very accurate technique, but the mass spectrometer does require careful calibration e.g. relative to carbon-12 isotope given an arbitrary value of 12.0000 atomic mass units and quality instruments rarely make a mistake.

The analysis can be done quickly AND continuously.

A sampling system connected to a mass spectrometer system can monitor pollution or a chemical production process 24/7!

A mass spectrometer can be linked to other analytical instruments e.g. you can set up a mass spectrometer to sample the separate molecules exiting from a gas chromatograph column. see section (d)

As a result of improved technology, the applications of mass spectrometry include forensic toxicology, drug development and identification of active ingredients, drug testing and discovery, food contamination detection, pesticide residue analysis in water or soil samples and protein identification.

It is possible to detect extremely low levels of organic compounds in the most complex of mixtures, including sports anti-doping analysis and chemical warfare agent detection


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(c) Indentifying a molecule from the molecular ion peak and fragmentation pattern

You can identify a molecular formula using a high resolution mass spectrometer from a very accurate molecular mass.

However, if isomers are possible, you need more data to ascertain its molecular structure.

It is possible to investigate aspects of a molecular structure from the mass spectrum fragmentation pattern.

If the molecule is known and the mass spectrum obtained for a pure sample, identification of an organic molecule is possible from its unique fragmentation patterns (a mass spectra fingerprint) - but the database data must be obtained under the same experimental conditions i.e. the same instrument settings on the mass spectrometer.

For examples of identifying molecular formula from the molecular ion peak see

Isotopic masses and accurate molecular ion peaks to identify molecules and molecular formulae

show a comparison of spectra e.g. isomers


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(d) Analysis and identification using gas chromatography linked with mass spectrometry (GC-MS)

The diagram below shows how a gas chromatograph can be linked to a mass spectrometer.

The chromatographic column coating (stationary immobile phase surface) separates the components in the mixture as they are carried along by the carrier gas (mobile phase).

The detector (many types) measures the amount of each component as they come through the column and simultaneously a sample can be tapped off to the mass spectrometer.

(I've shown the sampling for the mass spectrum immediately after the detector, but if it was a flame ionization detector, you would have to sample immediately before the detector).

diagram of mass spectrometer linked to a gas chromatograph GC machine column carrier gas detector sampling system identifying organic molecule in a mixture

Each component molecule can be identified from the very accurate molecular ion peak m/z and the fragmentation pattern, assuming the molecule is known in the database.

Even if it cannot be identified, the molecular formula can be obtained from a very accurate m/z value for the parent molecular [M]+ ion.

High temperature gas chromatography can be used to analyse for large molecules including fats and oils, so finds a use in developing biofuels.

Fragrances - perfumes can be developed by analysing natural oils from plants.

In astrochemistry GC-MS systems were taken to Mars by the Viking program. Venera 11 and 12 and Pioneer Venus analysed the atmosphere of Venus with GC-MS. The Huygens probe of the Cassini–Huygens mission landed one GC-MS on Saturn's largest moon, Titan.  The MSL Curiosity rover's sample analysis at Mars (SAM) instrument contains both a gas chromatograph and quadrupol mass spectrometer that can be used in tandem as a GC-MS. The material in the comet 67P/Churyumov–Gerasimenko was analysed by the Rosetta mission with a chiral GC-MS in 2014.

In clinical medicine, dozens of congenital metabolic diseases also known as inborn errors of metabolism (IEM) are now detectable by newborn screening tests, especially the testing using gas chromatography–mass spectrometry.

GC-MS can determine compounds in urine even in minor concentration.

These compounds are normally not present but appear in individuals suffering with metabolic disorders.

This is increasingly becoming a common way to diagnose IEM for earlier diagnosis and institution of treatment eventually leading to a better outcome.

It is now possible to test a newborn for over 100 genetic metabolic disorders by a urine test at birth based on GC-MS.

In combination with isotopic labeling of metabolic compounds, the GC-MS is used for determining metabolic activity.

Most applications are based on the use of 13C as the labelling and the measurement of 13C-12C ratios with an isotope ratio mass spectrometer (IRMS); an MS with a detector designed to measure a few select ions and return values as ratios.

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Key words & phrases: Explaining how to use gas chromatography and mass spectroscopy in tandem - diagram explaining how to connect a gas chromatograph to a mass spectrometer.


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