Principles of mass spectrometry. a MALDI-TOF mass spectrometer. The sample is co-crystallised with matrix molecules as a dry sample on the plate. The peptides are brought to an ionised gas phase by a laser pulse. b The ionised peptides are analysed in the time-of-flight (TOF) unit in the mass spectrometer giving a peptide mass fingerprint. c If the sample is pure enough, the peptide mass fingerprint can be used to search DNA and protein databases for identification. d Tandem mass spectrometry (MS/MS) as obtained by a Q-TOF mass spectrometer. The sample is ionised at atmospheric pressure by electrospray ionisation (ES source). The ions enter the vacuum system through the sampling cone and, in the quadrupole section ions, of a particular m/z are selected and fragmented in the collision cell. e In the collision cell, peptides are mainly fragmented at the peptide bonds producing b type (blue) and y type (red) ions. The masses of the resulting peptide fragments are measured in the TOF unit. f Example of a collision-induced spectrum with the amino acid sequence given as detected from the N-terminal (b type ions) and from the C-terminal (y type ions). Reprinted from Honoré et al.  with permission of John Wiley & Sons, Inc. The mass fingerprint (C) is reprinted from Honoré  with permission of Expert Reviews Ltd.