Mass Spectrometers measure the weights of molecules. This is typically done by electric and magnetic fields in a vacuum. In order to measure the masses of the molecules, the ions must be ionized and either formed in the vacuum or transfer to the vacuum.

The ionization usually takes place in the mass spectrometer source. The source is designed for the ionization method that is going to be uesd. On some instruments the ionization source can be changed for the ionization method. The choice of the ionization method is determine by the nature of the molecule. Some molecules may be ionized by multiple types of ionization methods; however, with some molecules, the mass spectroscopist will have to try many ionization methods to ionize the molecule.  Knowledge of the ionization methods and the molecules could help reduce the time the mass spectroscopist needs to find the correct ionization method.

The ions formed in the source are transferred to the analyzer, which is the heart of the spectrometer. The analyzer uses magnetic and electric fields to measure the mass to charge ratio of the ion. The compatibility of the analyzer to specific ionization sources vary significantly depending on the type of analyzer. This compatibility issue comes from the fact that some analyzers prefer to form ions in pulses while other analyzers prefer ions to be formed continuously. In addition, each analyzer has its own characteristics for such parameters as resolution, sensitivity, and speed of acquisition. Another feature of analyzers is that some may be operated in such a way to increase the sensitivity by increasing the selectivity.  Often times, a compromise is needed in the choice of analyzer to use.

Finally, the ions are detected. This is usually done by sending the ions into an electron multiplier or a micro channel plate, which multiplies the current and sends it on to a computer that plots the current vs. the mass to charge ratio. One other method of detection is by image current, which are used on FTMS analyzers (both ion cyclotron resonance and orbitrap based instruments). Image current detection, detects the ions going around the instrument in pattern by the induced current on electrodes, this current measures the frequency of the pattern, which the computer uses to come up with the mass spectrum, which is the mass to charge ratio vs. intensity graph.