Tools of the Trade: Mass Spectrometry

So, you’re watching an episode of CSI Miami and after a series of bad puns, Horatio and the gang come across a mystery substance that they need identified. They then put a sample into a Magic Chemical Identifying Machine™. Two beeps and a boop later, they know exactly what the mystery chemical is. For once, this is not all Hollywood magic. The Magic Chemical Identifying Machine™ is actually two distinct machines linked together: a gas chromatograph and a mass spectrometer.

Today, we’ll focus on the mass spectrometer device (stay tuned for the chromatography post!). A mass spectrometer is an extremely sensitive device that can tell you the mass of charged particles called ions. Gaseous molecules enter the mass spectrometer, but they are neutral and unable to be detected. So how exactly does the mass spec. make neutral molecules into analyzable ions? With a handy-dandy electron beam of course! When the electrons from the electron beam hit the molecule, an additional electron is stripped from the molecule, which results in a +1 charge on the molecule.

Schematic of a typical mass spectrometer

The typical mass spectrometer uses an array of electrodes called a quadrupole. These electrodes are capable of generating very precise electric fields. The computer attached to the mass spectrometer makes the quadrupole rapidly sweep through different electric fields. At any moment in time, only one exact ion mass is capable of moving straight through the machine. All other masses are deflected harmlessly onto the walls of the device. When an ion hits the analyzer in the mass spectrometer, the small current produced is measured as a signal. By matching the time of impact with the electric field that would cause the impact (and using some clever physics), the computer is able to determine the mass of the ion.

But, wait a minute, how can this information be used to identify specific molecules? Recall the +1 ion generated by the handy-dandy electron beam (I’m quite sure that is the technical term). For most molecules, this “molecular ion” is very unstable. The unstable ion usually fragments into smaller, more stable ions. One might think that fragmentation is a bad thing, but in fact most molecules generate a “fingerprint” of fragment ions. By cross-referencing the fingerprint of the unknown with that of known compounds, we can identify the unknown compound. Now that Horatio knows what the unknown compound is, he can catch the killer and wrap up the case with a perfect one-liner.

Source: 

http://en.wikipedia.org/wiki/Mass_spectrometry