title: Sequence scrambling in shotgun proteomics is negligible.
abstract: 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.
authors.affiliation: Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Anton A
authors.initials: AA
authors.lastname: Goloborodko
authors.forename: Mikhail V
authors.initials: MV
authors.lastname: Gorshkov
authors.forename: David M
authors.initials: DM
authors.lastname: Good
authors.forename: Roman A
authors.initials: RA
authors.lastname: Zubarev
mesh_terms: D030562:Databases, Protein; D010446:Peptide Fragments / Q000737:chemistry; D010449:Peptide Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010446:Peptide Fragments