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

Journal Article · Fri Jan 01 04:00:00 EST 2010 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-11-118· OSTI ID:978273

Pan, Chongle ^[1]; Park, Byung H ^[1]; McDonald, W Hayes ^[1]; Banfield, Jillian F. ^[2]; Verberkmoes, Nathan C ^[1]; Samatova, Nagiza F ^[1]

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1. ORNL
2. University of California, Berkeley

High-resolution tandem mass spectra can now readily be acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. In this study, a new de novo sequencing algorithm, Vonode, has been developed specifically for such high-resolution tandem mass spectra. To fully exploit the high mass accuracy, sparse noise, and low background of these spectra, a unique scoring system is used to evaluate sequence tags based mainly 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%. The performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, especially in term of the number of de novo sequenced spectra.

• Research Organization: Oak Ridge National Laboratory (ORNL); Center for Computational Sciences
• Sponsoring Organization: ORNL LDRD Director's R&D; SC USDOE - Office of Science (SC)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 978273
• Journal Information: BMC Bioinformatics, Journal Name: BMC Bioinformatics Vol. 11
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
ACCURACY
ALGORITHMS
DATA ANALYSIS
DNA SEQUENCING
MASS SPECTRA
MASS SPECTROSCOPY
PEPTIDES
PERFORMANCE
RESIDUES
RHODOPSEUDOMONAS