A mass spectrometer determines the mass of a molecule by measuring the mass-to-charge ration (m/z) of its ion. Ions are generated by inducing either the loss or gain of a charge from a neutral species. Once formed, ions are electrostatically directed into a mass analyzer where they are separated according to m/z and finally detected. The result of molecular ionization, ion separation, and ion detection is a spectrum that can provide highly accurate molecular mass and mass structural information.

An analyte is a collection of peptides derived protein after digestion. Two types of analyses are carried out on an analyte:

• Analysis of intact peptide ions - PMF
• Analysis of fragmented ions – PFF

There are several different mass spectrometers. However, all sample molecules undergo the same processes regardless of instrument configuration. Sample molecules are introduced into the instrument through a sample inlet. Once inside the instrument, the sample molecules are converted to ions in the ionization source, before being electrostatically propelled into the mass analyzer. Ions are then separated according to their m/z within the mass analyzer. The detector converts the ion energy into electrical signals, which are then transmitted to a computer.