Collision-activated dissociation (CAD), the most widely used peptide ion fragmentation technique for peptide sequence analysis by tandem mass spectrometry, works great for small peptides but is problematic for labile posttranslational modifications (PTMs). In the last decade, researchers have developed an alternative, electron capture dissociation (ECD), which involves reacting multiply-protonated peptides with thermal electrons, and provides random cleavage of the peptide backbone while leaving most labile PTMs attached and intact. The drawback: Mixing cations and electrons requires a high magnetic field, only present in Fourier transform ion cyclotron resonance mass spectrometers, which few labs can afford.

Another group has since developed an ion/ion analog of ECD, electron transfer dissociation (ETD), that is compatible with widely used and more affordable RF ion trap mass analyzers. Ion traps' radio frequency (RF) electric fields can confine both cations and anions, but not cations and vastly lighter electrons, so ETD uses specially-chosen anions to act...

1. Peptide cations, injected down the axis of the ion trap, collect in the central section. Auxiliary fields radially eject all cations (grey) except those with mass-to-charge (m/z) range of the chosen peptide ion species (blue). 2. Adjusting direct current (DC) bias potentials sequesters peptide cations in the trap's front segment; fluoranthene ions, efficient electron transfer reagents, are injected through the back; manipulating the applied fields expels anions not matching reagent ion m/z.
3. RF voltages applied to electrodes at both ends of the trap align the DC bias potentials on all trap electrodes; cations and anions mix freely, initiating the reaction. 4. The cations, a mix of leftover peptide precursors (blue) and dissociation product (green), are sequestered in the center segment by depressing bias potential there. Removing RF voltage at the end electrodes eliminates anions from the trap.
5. Ramping the intensity of RF trapping and auxiliary fields gives the product ion mass spectrum; residual precursor cations and product cations are radially ejected in m/z order through the trap rod electrodes to ion detectors. (Or, trapped ions can be further manipulated or transferred axially to another m/z analyzer.)

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