title: Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra.
abstract: We report an automated method for determining charge states from high-resolution mass spectra. Fourier transforms of isotope packets from high-resolution mass spectra are compared to Fourier transforms of modeled isotopic peak packets for a range of charge states. The charge state for the experimental ion packet is determined by the model isotope packet that yields the best match in the comparison of the Fourier transforms. This strategy is demonstrated for determining peptide ion charge states from "zoom scan" data from a linear quadrupole ion trap mass spectrometer, enabling the subsequent automated identification of singly- through quadruply-charged peptide ions, while reducing the numbers of conflicting identifications from ambiguous charge state assignments. We also apply this technique to determine the charges of intact protein ions from LC-FTICR data, demonstrating that it is more sensitive under these experimental conditions than two existing algorithms. The strategy outlined in this paper should be generally applicable to mass spectra obtained from any instrument capable of isotopic resolution.
authors.affiliation: Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.affiliation: Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Manesh B
authors.initials: MB
authors.lastname: Shah
authors.affiliation: Chemical Sciences Division, Oak Ridge National Laboratory, MS 6131, P.O. Box 2008, 37831-6131, Oak Ridge, TN, USA.
authors.forename: Michael Brad
authors.initials: MB
authors.lastname: Strader
authors.affiliation: Chemical Sciences Division, Oak Ridge National Laboratory, MS 6131, P.O. Box 2008, 37831-6131, Oak Ridge, TN, USA.|Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, 1060 Commerce Park, 37830, Oak Ridge, TN.
authors.forename: Heather M
authors.initials: HM
authors.lastname: Connelly
authors.affiliation: Chemical Sciences Division, Oak Ridge National Laboratory, MS 6131, P.O. Box 2008, 37831-6131, Oak Ridge, TN, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.affiliation: Chemical Sciences Division, Oak Ridge National Laboratory, MS 6131, P.O. Box 2008, 37831-6131, Oak Ridge, TN, USA. hurstgb@ornl.gov.
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Hurst
mesh_terms: D000465:Algorithms; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D003198:Computer Simulation; D005583:Fourier Analysis; D007477:Ions; D007553:Isotope Labeling / Q000379:methods; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D012815:Signal Processing, Computer-Assisted; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D055672:Static Electricity
chemical_list: D007477:Ions; D010455:Peptides; D011506:Proteins