A machine for performing mass spectrometry on chemical samples

A mass spectrometer consists of sample chamber, in which the sample is heated by untill it is gaseous, and then bombarded with electrons from an electron gun. The gun "knocks" electrons off the sample, turning the molecules into charged ions. The ions are then accelerated by an electric field and deflected by a magnetic field. Heavier ions are deflected less than lighter ions, and so the exact mass of the ions is determined by where they hit the detector. This produces a mass spectrum, which shows the mass and relative proportion of the different ions that were in the sample enabling the exact contents of the sample to be determined

A more recent innovation is the use of "time of flight" mass spectrometry, which measures the time of flight taken by each of the ions. Since heavier ions accelerate less, they will take longer and the mass spectrum can be determined by the time taken by each ion.

A major problem with mass spectrometry is that it can fragment molecules, breaking large molecules into smaller ones. Although this can be useful, most of the time it confuses the mass spectrum. The major advantage of time of flight spectrometry is that it produces less fragmentation.

More advanced spectrometers can perform a number of aditional functions, such as protein mass spectrometers, which actually use two spectrometers, to fragment the protein and analyse the amino acid fragments or mass spectrometers linked into a gas chromagraph, which separates samples prior to analysis

Fragmentation in mass spectrometry is a feature, not a drawback. Determination of the molecular ion peak (M peak), while not always trivial (and sometimes the peak is not even present), is less important than determination of the structure of the compound.

Mass spectrometers allow this to be done quite easily and in a wonderful way: shooting electrons through the electron gun into the chamber containing the sample breaks chemical bonds in the sample. This creates ions of various molecular weights which are detected as the magnetic field is altered to put different masses of charged particles into the detector at different field strengths, generating a spectrum.

For example, a peak of weight 29 is characteristic of an ethyl group (2 carbons + 5 hydrogens = 24 + 5 = 29), rather than 30 as it is a cation (different from ethane in that it has one fewer hydrogen). This means that, somewhere on your molecule, there is an ethyl group, and how big the peak is tells you how much that fragment is being generated and therefore what its chemical environment is.

Another great application is looking at the M+1, M+2, and higher peaks. What's going on here, you ask? Ion fragments bigger than the original molecule? What is going on is you are seeing the fraction of the sample containing such atoms as carbon-13 (a carbon with one more neutron than carbon-12, the most common form). Why is this useful? You can find out from this about how many carbons, bromines, chlorines, and so forth are in the molecule by simple inspection of a small part of the mass spectrum, giving you a good start on compound identification. Just look at the relative size of the peaks, and compare them to a table of relative abundances of higher-mass isotopes of the elements which might be in the compound.

For a more elaborate explanation of the joys of mass spectrometers, I refer you to such books as Pavia et al's Introduction to Spectroscopy. Suffice it to say, though, that mass spectroscopy (itself a misnomer, as mass spectrometers aren't really spectrometers in the strictest sense of the word) is one of the most powerful tools available to modern chemists for compound identification, and, together with NMR, can provide a complete picture of pretty much any molecule.

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