Bern M, Kil YJ, Tang W, Becker C, Frese CK, Altelaar M, Mohammed S, Heck AJR, Syka J, Bomgarden R, Viner R.
ASMS 2013 Poster
Electron transfer dissociation (ETD) and beam-type collision-induced dissociation (HCD) are combined in a new fragmentation method called EThcD on Thermo Scientific Orbitrap instruments. This method first applies ETD in the linear ion trap and then transfers all the ions, both precursors and products, to the HCD collision cell for further fragmentation. An EThcD spectrum includes b-, c-, y-, and z-ions, and is roughly equivalent to the union of an ETD and an HCD spectrum. EThcD has been shown to give more complete fragmentation of unmodified peptides than either ETD or HCD alone [Frese et al, 2012], and to give more confident site localization of phosphorylations [Frese et al, 2013], yet many basic questions about the fragmentation method remain. In this poster we give statistical and anecdotal answers to these questions:
• Which fragmentation mode (ETD, HCD, or EThcD) gives the most identifications?
• How complete is EThcD fragmentation? Which ions predominate?
• How do EThcD spectra vary with precursor charge and HCD collision energy?
• Does EThcD give good fragmentation even on multiply phosphorylated peptides?
• Does an EThcD spectrum of an N-glycopeptide show the glycan fragmentation of an HCD spectrum along with the peptide fragmentation of an ETD spectrum?
• Does an EThcD spectrum of an O-glycopeptide allow for modification site localization?
Protein Metrics Inc., San Carlos, CA
United States
