A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.

Abstract:

BACKGROUND:High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. RESULTS:In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. CONCLUSIONS:Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode.

journal_name

BMC Bioinformatics

journal_title

BMC bioinformatics

authors

Pan C,Park BH,McDonald WH,Carey PA,Banfield JF,VerBerkmoes NC,Hettich RL,Samatova NF

doi

10.1186/1471-2105-11-118

subject

Has Abstract

pub_date

2010-03-05 00:00:00

pages

118

issn

1471-2105

pii

1471-2105-11-118

journal_volume

11

pub_type

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