A Framework of De Novo Peptide Sequencing for Multiple Tandem Mass Spectra
peer-reviewed · IEEE Transactions on NanoBioscience · 2015
| Date | 2015-06-01 |
| Type | peer-reviewed |
| Venue | IEEE Transactions on NanoBioscience |
| Publisher | Institute of Electrical and Electronics Engineers (IEEE) |
| Contribution | algorithm |
| DOI | 10.1109/tnb.2015.2419194 |
| Citations (OpenAlex) | 5 |
Abstract
With tandem mass spectrometry (MS/MS), spectra can be generated by various fragmentation techniques including collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), electron capture dissociation (ECD), electron transfer dissociation (ETD) and so on. At the same time, de novo sequencing using multiple spectra from the same peptide generated by different fragmentation techniques is becoming popular in proteomics studies. The focus of this study is the use of paired spectra from CID (or HCD) and ECD (or ETD) fragmentation because of the complementarity between them. We present a de novo peptide sequencing framework for multiple tandem mass spectra, and apply it to paired spectra sequencing problem. The performance of the framework on paired spectra is compared to another successful method named pNovo+. The results show that our proposed method outperforms pNovo+ in terms of full length peptide sequencing accuracy on three pairs of experimental datasets, with the accuracy increasing up to 13.6% compared to pNovo+.
Methods and tools
- Multiple-spectra de novo framework: A de novo sequencing framework that combines spectra of the same peptide from complementary fragmentation methods such as CID/HCD with ECD/ETD.
Methods it uses
- pNovo+: Complementary HCD + ETD spectra
Cites (12)
- NovoGMET: De Novo Peptide Sequencing Using Graphs with Multiple Edge Types (GMET) for ETD/ECD Spectra (2014) crossref
- NovoHCD: De novo Peptide Sequencing From HCD Spectra (2014) crossref
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010) crossref
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry (2010) crossref
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) crossref
- DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring (2008) crossref
- Proteomics-Grade de Novo Sequencing Approach (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) crossref
- Algorithms for de novo peptide sequencing using tandem mass spectrometry (2004) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
Cited by (3)
- De novo sequencing of multiple SILAC-based tandem mass spectra (2022) crossref
- Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics (2019) both
- Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs (2016) both