A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry
- ORNL
- 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 Lab. (ORNL), Oak Ridge, TN (United States). National Center for Computational Sciences (NCCS)
- Sponsoring Organization:
- USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC)
- DOE Contract Number:
- DE-AC05-00OR22725
- OSTI ID:
- 978273
- Journal Information:
- BMC Bioinformatics, Vol. 11
- Country of Publication:
- United States
- Language:
- English
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