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Chemistry LibreTexts

Mass spectrometry 1

In mass spectrometry (MS), we are interested in the mass - and therefore the molecular weight - of our compound of interest, and often the mass of fragments that are produced when the molecule is caused to break apart. There are many different types of MS instruments, but they all have the same three essential components.  First, there is an ionization source, where the molecule is given a positive electrical charge, either by removing an electron or by adding a proton. Depending on the ionization method used, the ionized molecule may or may not break apart into a population of smaller fragments. In the figure below, some of the sample molecules remain whole, while others fragment into smaller pieces.

Next in line there is a mass analyzer, where the cationic fragments are separated according to their mass. Finally, there is a detector, which detects and quantifies the separated ions.



One of the more common types of MS techniques used in the organic laboratory is electron ionization.  In the ionization source, the sample molecule is bombarded by a high-energy electron beam, which has the effect of knocking a valence electron off of the molecule to form a radical cation.  Because a great deal of energy is transferred by this bombardment process, the radical cation quickly begins to break up into smaller fragments, some of which are positively charged and some of which are neutral.  The neutral fragments are either adsorbed onto the walls of the chamber or are removed by a vacuum source.  In the mass analyzer component, the positively charged fragments and any remaining unfragmented molecular ions are accelerated down a tube by an electric field. This tube is curved, and the ions are deflected by a strong magnetic field.  Ions of different mass to charge (m/z) ratios are deflected to a different extent, resulting in a ‘sorting’ of ions by mass (virtually all ions have charges of z =  +1, so sorting by the mass to charge ratio is the same thing as sorting by mass).  A detector at the end of the curved flight tube records  and quantifies the sorted ions.

Below is typical output for an electron-ionization MS experiment (MS data below is derived from the Spectral Database for Organic Compounds, a free, web-based service provided by AIST in Japan.


The sample is acetone.  On the horizontal axis is the value for m/z (as we stated above, the charge z is almost always +1, so in practice this is the same as mass).  On the vertical axis is the relative abundance of each ion detected.  On this scale, the most abundant ion, called the base peak, is set to 100%, and all other peaks are recorded relative to this value. For acetone, the base peak corresponds to a fragment with m/z = 43 - .  The molecular weight of acetone is 58, so we can identify the peak at m/z = 58 as that corresponding to the molecular ion peak, or parent peak.  Notice that there is a small peak at m/z = 59: this is referred to as the M+1 peak.  How can there be an ion that has a greater mass than the molecular ion?  Simple: a small fraction - about 1.1% - of all carbon atoms in nature are actually the 13C rather than the 12C isotope. The 13C isotope is, of course, heavier than 12C  by 1 mass unit.  In addition, about 0.015% of all hydrogen atoms are actually deuterium, the 2H isotope.   So the M+1 peak represents those few acetone molecules in the sample which contained either a 13C or 2H.   

The fragmentation of molecular ions into an assortment of fragment ions is a mixed blessing. The nature of the fragments often provides a clue to the molecular structure, but if the molecular ion has a lifetime of less than a few microseconds it will not survive long enough to be observed. Without a molecular ion peak as a reference, the difficulty of interpreting a mass spectrum increases markedly. Fortunately, most organic compounds give mass spectra that include a molecular ion, and those that do not often respond successfully to the use of milder ionization conditions. Among simple organic compounds, the most stable molecular ions are those from aromatic rings, other conjugated pi-electron systems and . Alcohols, ethers and highly branched generally show the greatest tendency toward fragmentation.


The mass spectrum of dodecane  illustrates the behavior of an unbranched alkane. Since there are no heteroatoms in this molecule, there are no non-bonding valence shell electrons. Consequently, the radical cation character of the molecular ion (m/z = 170) is delocalized over all the covalent bonds. Fragmentation of C-C bonds occurs because they are usually weaker than C-H bonds, and this produces a mixture of alkyl radicals and alkyl carbocations. The positive charge commonly resides on the smaller fragment, so we see a homologous series of hexyl (m/z = 85), pentyl (m/z = 71), butyl (m/z = 57), propyl (m/z = 43), ethyl (m/z = 29) and methyl (m/z = 15) cations. These are accompanied by a set of corresponding alkenyl carbocations (e.g. m/z = 55, 41 &27) formed by loss of 2 H. All of the significant fragment ions in this spectrum are even-electron ions. In most alkane spectra the propyl and butyl ions are the most abundant.

The presence of a functional group, particularly one having a heteroatom Y with non-bonding valence electrons (Y = N, O, S, X etc.), can dramatically alter the fragmentation pattern of a compound. This influence is thought to occur because of a "localization" of the radical cation component of the molecular ion on the heteroatom. After all, it is easier to remove (ionize) a non-bonding electron than one that is part of a covalent bond. By localizing the reactive moiety, certain fragmentation processes will be favored. These are summarized in the following diagram, where the green shaded box at the top displays examples of such "localized" molecular ions. The first two fragmentation paths lead to even-electron ions, and the elimination (path #3) gives an odd-electron ion. Note the use of different curved arrows to show single electron shifts compared with electron pair shifts.


The charge distributions shown above are common, but for each cleavage process the charge may sometimes be carried by the other (neutral) species, and both fragment ions are observed. Of the three cleavage reactions described here, the alpha-cleavage is generally favored for nitrogen, oxygen and sulfur compounds. Indeed, in the spectra of 4-methyl-3-pentene-2-one and N,N-diethylmethylamine the major fragment ions come from alpha-cleavage.


The complexity of fragmentation patterns has led to mass spectra being used as "fingerprints" for identifying compounds. Environmental pollutants, pesticide residues on food, and controlled substance identification are but a few examples of this application. Extremely small samples of an unknown substance (a microgram or less) are sufficient for such analysis. The following mass spectrum of cocaine demonstrates how a forensic laboratory might determine the nature of an unknown street drug. Even though extensive fragmentation has occurred, many of the more abundant ions (identified by magenta numbers) can be rationalized by the three mechanisms shown above. Plausible assignments may be seen by clicking on the spectrum, and it should be noted that all are even-electron ions. The m/z = 42 ion might be any or all of the following: C3H6, C2H2O or C2H4N. A precise assignment could be made from a high-resolution m/z value (next section).



Molecules with lots of oxygen atoms sometimes show a small M+2 peak (2 m/z units greater than the parent peak) in their mass spectra, due to the presence of a small amount of 18O (the most abundant isotope of oxygen is 16O). Because  there are two abundant isotopes of both chlorine (about 75% 35Cl and 25% 37Cl) and bromine (about 50% 79Br and 50% 81Br), chlorinated and brominated compounds have very large and recognizable  M+2 peaks. Fragments containing both isotopes of Br can be seen in the mass spectrum of ethyl bromide: 



A common fragmentation pattern for larger carbonyl compounds is called the McLafferty rearrangement:


The mass spectrum of 2-hexanone shows a 'McLafferty fragment' at m/z = 58, while the propene fragment is not observed because it is a neutral species (remember, only cationic fragments are observed in MS). The base peak in this spectrum is again an acylium ion.


When alcohols are subjected to electron ionization MS, the molecular ion is highly unstable and thus a parent peak is often not detected.  Often the base peak is from an ‘oxonium’ ion.



Other functional groups have predictable fragmentation patterns as well. By carefully analyzing the fragmentation information that a mass spectrum provides, a knowledgeable spectrometrist can often ‘put the puzzle together’ and make some very confident predictions about the structure of the starting sample.


The mass spectrum of an aldehyde gives prominent peaks at m/z = 59 (12%, highest value of m/z in the spectrum),  58 (85%), and 29 (100%), as well as others.  Propose a structure, and identify the three species whose m/z values were listed.



Gas Chromatography - Mass Spectrometry

Quite often, mass spectrometry is used in conjunction with a separation technique called gas chromatography (GC).  The combined GC-MS procedure is very useful when dealing with a sample that is a mixture of two or more different compounds, because the various compounds are separated from one another before being subjected individually to MS analysis.  We will not go into the details of gas chromatography here, although if you are taking an organic laboratory course you might well get a chance to try your hand at GC, and you will almost certainly be exposed to the conceptually analogous techniques of thin layer and column chromatography.  Suffice it to say that in GC, a very small amount of a liquid sample is vaporized, injected into a long, coiled metal column, and pushed though the column by helium gas.  Along the way, different compounds in the sample stick to the walls of the column to different extents, and thus travel at different speeds and emerge separately from the end of the column.  In GC-MS, each purified compound is sent directly from the end of GC column into the MS instrument, so in the end we get a separate mass spectrum for each of the compounds in the original mixed sample.  Because a compound's MS spectrum is a very reliable and reproducible  'fingerprint', we can instruct the instrument to search an MS database and identify each compound in the sample.

The extremely high sensitivity of modern GC-MS instrumentation makes it possible to detect and identify very small trace amounts of organic compounds.  GC-MS is being used increasingly by environmental chemists to detect the presence of harmful organic contaminants in food and water samples.   Airport security screeners  also use high-speed GC-MS instruments to look for residue from bomb-making chemicals on checked luggage.