title: HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.
abstract: Peptide sequence matching algorithms used for peptide identification by tandem mass spectrometry (MS/MS) enumerate theoretical peptides from the database, predict their fragment ions, and match them to the experimental MS/MS spectra. Here, we present an approach for scoring MS/MS identifications based on the high mass accuracy matching of precursor ions, the identification of a high intensity b1 fragment ion, and partial sequence tags from phenylthiocarbamoyl-derivatized peptides. This derivatization process boosts the b1 fragment ion signal, which turns it into a powerful feature for peptide identification. We demonstrate the effectiveness of our scoring system by implementing it on a computational tool called "HI-bone" and by identifying mass spectra of an Escherichia coli sample acquired on an Orbitrap Velos instrument using Higher-energy C-trap dissociation. Following this strategy, we identified 1614 peptide spectrum matches with a peptide false discovery rate (FDR) below 1%. These results were significantly higher than those from Mascot and SEQUEST using a similar FDR.
authors: Department of Proteomics, Center for Genetic Engineering and Biotechnology, Cubanacán, Playa, Ciudad de la Habana, Cuba.
authors: Yasset
authors: Y
authors: Perez-Riverol
authors: Aniel
authors: A
authors: Sánchez
authors: Jesus
authors: J
authors: Noda
authors: Diogo
authors: D
authors: Borges
authors: Paulo Costa
authors: PC
authors: Carvalho
authors: Rui
authors: R
authors: Wang
authors: Juan Antonio
authors: JA
authors: Vizcaíno
authors: Lázaro
authors: L
authors: Betancourt
authors: Yassel
authors: Y
authors: Ramos
authors: Gabriel
authors: G
authors: Duarte
authors: Fabio C S
authors: FC
authors: Nogueira
authors: Luis J
authors: LJ
authors: González
authors: Gabriel
authors: G
authors: Padrón
authors: David L
authors: DL
authors: Tabb
authors: Henning
authors: H
authors: Hermjakob
authors: Gilberto B
authors: GB
authors: Domont
authors: Vladimir
authors: V
authors: Besada
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry; D006801:Humans; D007477:Ions / Q000737:chemistry; D017879:Isothiocyanates / Q000737:chemistry*; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D029968:Escherichia coli Proteins; D007477:Ions; D017879:Isothiocyanates; D010455:Peptides; C005441:phenylisothiocyanate