title: On the benefits of acquiring peptide fragment ions at high measured mass accuracy.
abstract: The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the "C-trap" in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated with this data acquisition mode. It is therefore concluded that acquisition of tandem mass spectral data with high measured mass accuracy and resolution is a competitive alternative to "classical" data acquisition strategies, especially in situations of complex searches from large databases, searches for modified peptides, or for peptides resulting from unspecific cleavages.
authors.affiliation: Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Scherl
authors.forename: Scott A
authors.initials: SA
authors.lastname: Shaffer
authors.forename: Gregory K
authors.initials: GK
authors.lastname: Taylor
authors.forename: Patricia
authors.initials: P
authors.lastname: Hernandez
authors.forename: Ron D
authors.initials: RD
authors.lastname: Appel
authors.forename: Pierre-Alain
authors.initials: PA
authors.lastname: Binz
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
mesh_terms: D007477:Ions; D010449:Peptide Mapping / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*
chemical_list: D007477:Ions