HI-Bone: A Scoring System for Identifying Phenylisothiocyanate-Derivatized Peptides Based on Precursor Mass and High Intensity Fragment Ions

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• 作者：Yasset Perez-Riverol ; Aniel S谩nchez ; Jesus Noda ; Diogo Borges ; Paulo Costa Carvalho ; Rui Wang ; Juan Antonio Vizca铆no ; L谩zaro Betancourt ; Yassel Ramos ; Gabriel Duarte ; Fabio C.S. Nogueira ; Luis J. Gonz谩lez ; Gabriel Padr贸n ; David L. Tabb ; Henning Hermjakob ; Gilberto B. Domont ; Vladimir Besada
• 刊名：Analytical Chemistry
• 出版年：2013
• 出版时间：April 2, 2013
• 年：2013
• 卷：85
• 期：7
• 页码：3515-3520
• 全文大小：333K
• 年卷期：v.85,no.7(April 2, 2013)
• ISSN：1520-6882

文摘

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 鈥淗I-bone鈥?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.