The BioPharma Finder application supports the following fragmentation methods for MS data:

  • CID (collision-induced dissociation): Molecular ions are accelerated to high kinetic energy in the vacuum of a mass spectrometer and then allowed to collide with neutral gas molecules such as helium, nitrogen, or argon. The collision breaks the bonds and fragments the molecular ions into smaller pieces.
  • HCD (higher-energy collision-induced dissociation): Ion optics accelerate the precursor ions into a high-pressure cell, where they collide with nitrogen gas. The projectile ion has laboratory-frame translation energy higher than 1 keV.
  • SID (surface-induced dissociation): Molecular ions collide with a target surface composed of a relatively rigid material to maximize fragmentation.
  • ETD (electron transfer dissociation): Singly charged reagent anions transfer an electron to protonated peptides within an ion trap mass analyzer to induce fragmentation. ETD cleaves randomly along the peptide backbone while side chains and modifications, such as phosphorylation, are left intact. This method is used to fragment peptides and proteins.
  • ECD (electron capture dissociation): Protonated molecules are introduced to low-energy free electrons. Capture of the electrons releases electric potential energy and reduces the charge state of the ions by producing odd-electron ions, which easily fragment.
  • ETHCD (electron transfer higher-energy collision dissociation): Fragmentation is similar to HCD, but involves an initial electron-transfer dissociation step and produces additional b and y ions.
  • IRMPD (infrared multi-photon dissociation): An infrared laser is directed at the ions in the vacuum of the mass spectrometer. The target ions absorb multiple infrared photons until they reach more energetic states and begin to break bonds, resulting in fragmentation.
  • UVPD (ultraviolet photodissociation): Ultraviolet photons activate the proteins for fragmentation, providing ultra-high resolution for improved structural elucidation and quantitation of isobaric compounds.