title: De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.
abstract: There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS). Existing MS-based methods characterize a novel protein by assembling tandem mass spectra of overlapping peptides generated from multiple proteolytic digestions of the protein. Because each tandem mass spectrum covers only a short peptide of the target protein, the key to high coverage protein sequencing is to find spectral pairs from overlapping peptides in order to assemble tandem mass spectra to long ones. However, overlapping regions of peptides may be too short to be confidently identified. High-resolution mass spectrometers have become accessible to many laboratories. These mass spectrometers are capable of analyzing molecules of large mass values, boosting the development of top-down MS. Top-down tandem mass spectra cover whole proteins. However, top-down tandem mass spectra, even combined, rarely provide full ion fragmentation coverage of a protein. We propose an algorithm, TBNovo, for de novo protein sequencing by combining top-down and bottom-up MS. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass spectra are aligned to the scaffold to increase sequence coverage. Experiments on data sets of two proteins showed that TBNovo achieved high sequence coverage and high sequence accuracy.
authors.affiliation: Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis , 535 West Michigan Street, IT 475, Indianapolis, Indiana 46202, United States.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
authors.forename: Lennard J M
authors.initials: LJ
authors.lastname: Dekker
authors.forename: Si
authors.initials: S
authors.lastname: Wu
authors.forename: Martijn M
authors.initials: MM
authors.lastname: Vanduijn
authors.forename: Theo M
authors.initials: TM
authors.lastname: Luider
authors.forename: Nikola
authors.initials: N
authors.lastname: Tolić
authors.forename: Qiang
authors.initials: Q
authors.lastname: Kou
authors.forename: Mikhail
authors.initials: M
authors.lastname: Dvorkin
authors.forename: Sonya
authors.initials: S
authors.lastname: Alexandrova
authors.forename: Kira
authors.initials: K
authors.lastname: Vyatkina
authors.forename: Ljiljana
authors.initials: L
authors.lastname: Paša-Tolić
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000074323:Alemtuzumab; D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D061067:Antibodies, Monoclonal, Humanized / Q000737:chemistry; D024402:Carbonic Anhydrase II / Q000737:chemistry; D002417:Cattle; D008969:Molecular Sequence Data; D010449:Peptide Mapping; D020539:Sequence Analysis, Protein; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D061067:Antibodies, Monoclonal, Humanized; D000074323:Alemtuzumab; D024402:Carbonic Anhydrase II