Complementary fragementation:

CID is often used in proteomics, because it preferably leads to breaks of peptide bonds into b/y-ions and therefore divides proteins between residues. That allows the analysis of the resulting spectrum using the known masses of the residues. The resulting spectrum most reliably shows the b and y-ions of precursor peptides broken around the middle of the chain and the y-ions have stronger signals.

CID works by accelarating large ions using an electrical potential and colliding them with a neutral gas, e.g. helium. The force for the fragmentation comes from the kinetic energy of the accelerated ions.

ETD leads to different fragmentation patterns and leads to more complete fragmentation patterns for modified proteins. The resulting spectrum most reliaby shows c/z-ions with large masses when only a few residues are broken off of the precursor ion.

ETD employs radical anions, that transfer electrons to the precursor peptide and fragment the peptide chemically.

Complementary methods, that use more than one fragmentation technique, are used for de novo identification/sequencing of proteins. Because each fragmentation technique has its own preferences for types of fragments and fragmentation spectra, using more than one increases the probability of getting sufficient information about the residues at all positions of a peptide.

Other fragmentation techniques are ECD, Electron-capture dissociation, which prefers c/z-ions and SID, surface induced dissociation, which prefers b/y-ions.