A mass spectrometer operates according to a variety of designs, but all share some common features illustrated in this diagram:
Mass Spectrometer Schematic
  • The sample molecules are placed in the gas phase in a vacuum. In many cases, the sample is heated until its vapor pressure is high enough to observe a signal. Gas chromatography is another common method, but heavier (bigger) molecules require other techniques.
  • The sample molecules are converted to ions. In the most common "electron impact" method a high-energy electron beam knocks electrons off the molecules to form a radical cation. A gentler method of "chemical ionization" uses CH5+ (generated from electron impact on methane) to protonate the molecules.
  • The ions are accelerated in the desired direction using charged plates with the opposite electrical potential.
  • The ion stream enters a magnetic field. Ions are deflected to different degrees based primarily on their mass to charge ratio. The deflection can be controlled by altering either the magnetic field, or the accelerating voltage, or both.
  • Ions are detected by the charge they impart to a plate at the end of the system.
The information available in a mass spectrum contains many different pieces:
  1. Most ions collected will have a single charge, so the mass-to-charge ratio gives the actual mass of the molecule (since loss of the electron has a negligible effect of its mass). Very precise measurement of this ("High Resolution Mass Spectrometry--HRMS) provides a means of distinguishing among molecular formulas having the same nominal unit mass because of slightly different masses for protons and neutrons.
  2. Examination of slightly larger masses can reveal the presence of additional isotopes. The relative intensities of these (M+1)+, (M+2)+, etc., peaks can also be used to extract the molecular formula for M+.
  3. Often (usually, in electron impact ionization), the "parent ion" will undergo fragmentation reactions that are specific to structure. We can identify what's happening both by directly observing an ion with a smaller mass, and by subtracting that mass from the parent mass, identifying the neutral species (a radical, or a stable molecule) that has been lost. As in NMR spectral interpretation, this leads to a collection of "pieces" that we can reassemble to give us the structure of the molecule.
Please see the next page for example spectra and how to use all of this information.