Scaffold has the ability to recognize the the fragmentation mode used in MS experiments and the spectrum view will display the ions used in the determination of a peptide. Currently Scaffold does not annotate the spectrum itself with the collision type but does annotate the ions matched in the spectrum. The following documentation provides more information regarding collision types.
Note: CID and ETD are available on a wide variety of instruments, while HCD is available on Thermo Orbitrap instruments such as the Q-Exactive and Lumos.
CID (Collision Induced Dissociation):
Collision Induced Dissociation produces B ions and Y ions predominately, see screen shot below from Mascot (note Scaffold annotates ions as B or Y).
HCD (Collision Induced Dissociation):
Higher Energy Collision Induced Dissociation also produces B ions and Y ions predominately, see screenshot below from Proteome Discoverer (note Scaffold annotates ions as B or Y).
ETD (Electron Transfer Dissociation):
Electron Transfer Dissociation produces C ions and Z ions predominately, see screen shot below from Proteome Discoverer (note Scaffold annotates ions as C or Z).
Additional fragmentation types:
PQD: Pulsed Q Collision Inducted Dissociation available only of Thermo linear ion trap instruments produces B ions and Y ions similar to CID.
ETciD and EThcD: Are hybrid forms of ETD and CID/HCD and creates a combination of B and Y ions and C and Z ions and are available on Thermo instruments.
Search Engine Compatibility:
Scaffold reads in search engine results from a wide variety of programs and thus search engine compatibility is a key factor in determining whether spectra will be annotated in Scaffold; make sure to include the spectrum file, such such as an MGF, when applicable to visualize spectra in Scaffold.
- SEQUEST HT in Proteome Discoverer is compatible with all dissociation types
- Mascot is compatible with ETD, CID and HCD
- Most open source search engines are compatible with ETD, CID and HCD
- ZCore is a search engine specifically optomized to search spectra generated via ETD