ac3010007_si_001.pdf (49.86 kB)
Reduction in Database Search Space by Utilization of Amino Acid Composition Information from Electron Transfer Dissociation and Higher-Energy Collisional Dissociation Mass Spectra
journal contribution
posted on 2012-08-07, 00:00 authored by Thomas
A. Hansen, Fedor Kryuchkov, Frank KjeldsenWith high-mass accuracy and consecutively obtained electron
transfer
dissociation (ETD) and higher-energy collisional dissociation (HCD)
tandem mass spectrometry (MS/MS), reliable (≥97%) and sensitive
fragment ions have been extracted for identification of specific amino
acid residues in peptide sequences. The analytical benefit of these
specific amino acid composition (AAC) ions is to restrict the database
search space and provide identification of peptides with higher confidence
and reduced false negative rates. The 6706 uniquely identified peptide
sequences determined with a conservative Mascot score of >30 were
used to characterize the AAC ions. The loss of amino acid side chains
(small neutral losses, SNLs) from the charge reduced peptide radical
cations was studied using ETD. Complementary AAC information from
HCD spectra was provided by immonium ions. From the ETD/HCD mass spectra,
5162 and 6720 reliable SNLs and immonium ions were successfully extracted,
respectively. Automated application of the AAC information during
database searching resulted in an average 3.5-fold higher confidence
level of peptide identification. In addition, 4% and 28% more peptides
were identified above the significance level in a standard and extended
search space, respectively.