How a Mass Spectrometer Sorts and Weighs Molecules

Mass spectrometry (also called mass spec) provides valuable information about the structure of molecular compounds. Organic chemists can use a mass spectrometer to ionize — or "smash" — a molecular compound in gaseous form, sort the fragments, and then identify the molecule fragments based on their molecular weights.

To prepare the molecules for sorting and weighing, a sample containing an unknown compound is first injected into the mass spectrometer through an inlet (see the first figure), and is then vaporized by heating it under a vacuum. The vaporized sample is then pushed by an inert gas into the "smasher," where the sample is clobbered and broken into little bits.

After the molecules are smashed (thus becoming radical cations), some of them stay as they are and move through the spectrometer to the weigher. Those pieces that stay whole give a peak in the mass spectrum called the molecular ion peak, or M+ peak. This molecular ion peak tells you the molecular weight of the molecule, because losing an electron doesn't really change the weight of the molecule (it's like a tractor trailer losing a lug nut).

The molecular ion peak is the most important piece that's weighed by the mass spectrometer, because knowing the molecular weight of the unknown molecule is a very valuable piece of information when you're trying to determine its structure.

Some of the radical cations stay intact and lead to the molecular ion peak, but others break down spontaneously into smaller bits. Most commonly, the radical cations break into two pieces, one piece that's a neutral radical, and one piece that's a positively charged cation, as shown in the next figure. Only the charged cationic species is "seen" and weighed by the mass spectrometer. The neutral radicals are discarded and go undetected.

After the pieces have become charged by the smasher, they're sent through the weigher. This weigher, though, isn't like the scale that collects dust in your bathroom. Instead, because the fragments are charged, they can be weighed by accelerating them through the poles of a magnet.

When charged particles move through a magnetic field, they're deflected (pulled off course) by the magnetic field. All uncharged fragments are not deflected by the magnet and simply run into the walls of the spectrometer, never to be seen again. Therefore, only charged particles can hit the detector.

The weight of a fragment determines how much it will be deflected by the magnet. Light fragments are deflected a lot by the magnet, while heavier fragments are deflected less. With a low magnetic field strength, small particles will be bent the right amount by the spectrometer to hit the detector, while all the other fragments will crash and burn into the walls of the spectrometer.

With a larger magnetic field strength, larger particles will curve the right amount to hit the detector. By varying the magnetic field strength (which is proportional to the weight of the fragment), the weights of the fragments can be determined.