Goloborodko AA, Gorshkov MV, Good DM, Zubarev RA
J. Am. Soc. Mass Spectrom. 22 (7) 1121-1124 [2011-07-00; online 2011-04-15]
Analysis of 15,897 low-energy (CAD) and 10,878 higher-energy (HCD) collisional dissociation mass spectra of doubly protonated tryptic peptides taken with high resolution revealed that the rate of sequence scrambling due to b-ion cyclization is negligible (<1%) and can be safely ignored as a possible source of erroneous sequence assignment in shotgun proteomics. On the other hand, there is significant presence of normal (non-scrambled) internal fragments in HCD, which should be taken into account by MS/MS search engines.