De Novo Sequencing Assisted Approach for Characterizing Mixture MS/MS Spectra
peer-reviewed · IEEE Transactions on NanoBioscience · 2016
| Date | 2016-03-01 |
| Type | peer-reviewed |
| Venue | IEEE Transactions on NanoBioscience |
| Publisher | Institute of Electrical and Electronics Engineers (IEEE) |
| Contribution | algorithm |
| DOI | 10.1109/tnb.2016.2519841 |
| Citations (OpenAlex) | 2 |
Abstract
Extensive research has been conducted for the computational analysis of mass spectrometry based proteomics data. However, there are still remaining challenges, among which, one particular challenge is the low identification rate of the collected spectral data. A specific contributing factor is the existence of mixture spectra in the collected MS/MS spectra which are generated by the concurrent fragmentation of multiple precursors in one sequencing attempt. The quite frequently observed mixture spectra necessitates the development of effective computational approaches to characterize those non-conventional spectral data. In this research, we proposed an approach for matching the query mixture spectra with a pair of peptide sequences acquired from the protein database by incorporating a special de novo assisted filtration strategy. The experiment results on two different datasets of MS/MS spectra containing mixed ion fragments from multiple peptides demonstrated the efficiency of the integrated filtration strategy in reducing examination space and verified the effectiveness of the proposed matching scheme as well.
Methods and tools
- De novo assisted mixture spectrum characterization: Attacks the low identification rate caused by MIXTURE spectra, where more than one peptide co-fragments, by using de novo interpretation to characterize what the spectrum actually contains.
Cites (8)
- PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012) crossref
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) crossref
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref