NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra

peer-reviewed · IEEE/ACM Transactions on Computational Biology and Bioinformatics · 2017

peer-reviewed · IEEE/ACM Transactions on Computational Biology and Bioinformatics · 2017. Yan Yan et al. De novo peptide sequencing using tandem mass spectrometry (MS/MS) data has become a major computational…
Date 2017-03-01
Type peer-reviewed
Venue IEEE/ACM Transactions on Computational Biology and Bioinformatics
Publisher Institute of Electrical and Electronics Engineers (IEEE)
Contribution algorithm
DOI 10.1109/tcbb.2015.2389813
Citations (OpenAlex) 7
Venue 2-year citedness 2.33

Abstract

De novo peptide sequencing using tandem mass spectrometry (MS/MS) data has become a major computational method for sequence identification in recent years. With the development of new instruments and technology, novel computational methods have emerged with enhanced performance. However, there are only a few methods focusing on ECD/ETD spectra, which mainly contain variants of c -ions and z-ions. Here, a de novo sequencing method for ECD/ETD spectra, NovoExD, is presented. NovoExD applies a new form of spectrum graph with multiple edge types (called a GMET), considers multiple peptide tags, and integrates amino acid combination (AAC) and fragment ion charge information. Its performance is compared with another successful de novo sequencing method, pNovo+, which has an option for ECD/ETD spectra. Experiments conducted on three different datasets show that the average full length peptide identification accuracy of NovoExD is as high as 88.70 percent, and that NovoExD’s average accuracy is more than 20 percent greater on all datasets than that of pNovo+.

Authors

  1. Yan Yan · University of Saskatchewan, University of Western Ontario
  2. Anthony J. Kusalik · University of Saskatchewan
  3. Fang-Xiang Wu · University of Saskatchewan

Methods and tools

  • NovoExD: De novo peptide sequencing for ECD/ETD spectra, using a spectrum graph with multiple edge types for the c- and z-ion variants those spectra carry.

Cites (11)

Cited by (1)

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