A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry
peer-reviewed · BMC Bioinformatics · 2010
| Date | 2010-03-05 |
| Type | peer-reviewed |
| Venue | BMC Bioinformatics |
| Publisher | Springer Science and Business Media LLC |
| Contribution | algorithm |
| DOI | 10.1186/1471-2105-11-118 |
| Citations (OpenAlex) | 66 |
| Venue 2-year citedness | 4.50 |
Abstract
BACKGROUND: High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. RESULTS: In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily 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%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. CONCLUSIONS: Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode.
Methods and tools
- Vonode: High-throughput de novo sequencing approach for high-resolution shotgun proteomics spectra.
Cites (13)
- DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring (2008) both
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) both
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) both
- SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model (2003) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- A Suboptimal Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry (2003) both
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) both
- Implementation and Uses of Automated de Novo Peptide Sequencing by Tandem Mass Spectrometry (2001) both
- De novo peptide sequencing via tandem mass spectrometry (1999) both
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) both
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) both
Cited by (10)
- PepGo: a deep learning and tree search-based model for de novo peptide sequencing (2025) crossref
- De novo sequencing of proteins by mass spectrometry (2020) both
- Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation (2017) both
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs (2016) both
- De novo peptide sequencing using CID and HCD spectra pairs (2016) crossref
- Peptide de novo sequencing of mixture tandem mass spectra (2016) both
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- De Novo Sequencing and Homology Searching (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref