Instruments that trap ions in a magnetic and/or electric field play a very important role in the analysis of biomolecules. The two predominant instruments in the category of trapping instrument are the quadrupole ion trap mass spectrometer (QIT-MS) and the ion cyclotron resonance (ICR) MS. The latter is also commonly called Fourier transform MS (FT-MS). The QIT is an inexpensive, simple, and rugged MS used for various routine applications. The ICR-MS is an expensive, high-performance instrument with figures of merit for resolution and mass accuracy surpassing all other mass spectrometers. This chapter covers the basic principles of operation of these instruments, including the trapping/manipulation/detection of ions and various approaches used to activate ions to perform tandem mass spectrometry experiments.