The mass spectrometer. (A) Source. In ESI a liquid containing a protein/peptide mixture is passed through a high-voltage capillary tube resulting in charged peptides. In MALDI, a laser is used to excite a chemical matrix containing peptides leading to ejection of charged peptides into the gas phase. (B) Mass analyzers. The quadrupole uses both AC and DC current to affect the trajectory of incoming charged particles. The first quadrupole acts as a mass filter allowing only certain ions to pass into the second quadrupole, the collision cell, where they collide with a neutral gas, undergo fragmentation and enter into the third quadrupole that also acts as a mass filter. The ion-trap mass analyzer uses an AC voltage to "trap" ions. By increasing the AC amplitude, ions of increasing m/z ratio are ejected and measured by the detector. In Time of Flight (TOF), ions of different m/z values are injected into one end of the tube so that they each have approximately identical kinetic energy as they accelerate through the tube. Ions of less mass will reach the detector faster than those that are heavier. (C) Detector. As an ion strikes the surface of the electron multiplier detector, it causes the emission of electrons, which in turn results in the release of secondary electrons. This multiplication process results in the generation of 100 million electrons per incident ion. The arrival of the electron pulse registers as a single ion count.