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American Chemical Society, Analytical Chemistry, 7(85), p. 3515-3520, 2013

DOI: 10.1021/ac303239g

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

This paper is available in a repository.
This paper is available in a repository.

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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 HCD (Higher-energy C-trap dissociation). Following this strategy, we identified 1,614 Peptide Spectrum Matches (PSMs) with a peptide False Discovery Rate (FDR) below 1%. These results were significantly higher than those from Mascot and SEQUEST using a similar FDR.