TVNovo: De novo peptide sequencing for high resolution LTQ-FT mass spectrometry using virtual database searching

peer-reviewed · 2010 3rd International Conference on Biomedical Engineering and Informatics · 2010

peer-reviewed · 2010 3rd International Conference on Biomedical Engineering and Informatics · 2010. Han-Chang Sun et al. De novo peptide sequencing is one of the most challenging topics in the field of computational proteomics. In…
Date 2010-10-01
Type peer-reviewed
Venue 2010 3rd International Conference on Biomedical Engineering and Informatics
Publisher Institute of Electrical and Electronics Engineers (IEEE)
Contribution algorithm
DOI 10.1109/bmei.2010.5639865
Citations (OpenAlex) 1
Venue 2-year citedness 0.00

Abstract

De novo peptide sequencing is one of the most challenging topics in the field of computational proteomics. In this manuscript, a novel method based on virtual database searching is presented to improve the performance of de novo sequencing for the data from high resolution LTQ-FT mass spectrometry. Our method directly generates a virtual database from each spectrum and applies a search engine to match spectrum against the calculated virtual database. Two datasets from different sources are employed to compare our method to other existing de novo sequencing algorithms and the results show that our method outperforms other methods.

Authors

  1. Han-Chang Sun · Beijing Institute of Radiation Medicine, National University of Defense Technology
  2. Ji-Yang Zhang · Beijing Institute of Radiation Medicine, National University of Defense Technology
  3. Hui Liu · Beijing Institute of Radiation Medicine, National University of Defense Technology
  4. Wei Zhang (Changsha) · Beijing Institute of Radiation Medicine, National University of Defense Technology
  5. Chang-Ming Xu · Beijing Institute of Radiation Medicine, National University of Defense Technology
  6. Hai-Bin Ma · Beijing Institute of Radiation Medicine, National University of Defense Technology
  7. Hong-Wei Xie · National University of Defense Technology

Methods and tools

  • TVNovo: Turns de novo sequencing into a search problem by generating a VIRTUAL database per spectrum, enumerating the candidate sequences the precursor mass allows, then scoring them as a database search would. Built for high-resolution LTQ-FT data.

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