Date: 15 Apr 2011

Sequence Scrambling in Shotgun Proteomics is Negligible


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.