An ion trap mass spectrometer identifies molecules by ionizing and fragmenting them, then measuring the mass-to-charge ratio (m/z) of the observed ions to create a full-scan mass spectrum. Ions are created by electron ionization and are passed into the ion trap portion of the mass spectrometer where they can be manipulated further (for MS/MS measurements) or released to the detector. Because ions and molecules have time to interact with each other in the ion trap, ions and/or molecules can react to form new ions that are not normally seen in quadrupole mass spectra for the same compound. All ion trap mass spectrometers produce an M+1 (molecular weight+1) ion in the mass spectra of some molecules (those which have the right proton affinity). This M+1 ion does not appear in quadrupole, TOF, or sector MS data. Other molecules that cannot accept a proton will not have this M+1 ion. The abundance of this M+1 ion relative to other ions in the spectrum will vary with concentration. At low concentrations (~10-10¬¬0 ng on column, roughly), the M+1 peak is small and it grows as concentration increases, due to more ion-molecule interactions within the ion trap. Once concentration gets high enough (this conc. varies by molecule), the M+1 ion dwarfs the rest of the ions in the MS so they are not visible. At higher concentrations, the molecule will dimerize and an ion will be observed at a mass of 2M+1. This may indicate the upper bound of the dynamic range of the instrument. Some molecules will have a greater variance in the M+1 ion abundance than others. When this M+1 ion is present, ion trap mass spectra will not fully match mass spectra in the NIST library.

Ion trap mass spectrometers can be smaller than other types of mass spectrometers and do not require as high of a vacuum, so they can typically start up from an off position much faster than other types of mass spectrometers (~15 min). Air and water in the system do not affect the analysis as much as they do for other types of mass spectrometers. The scan range of an ion trap mass spectrometer is approximately one order of magnitude (e.g. m/z 40-400).