Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications
peer-reviewed · Journal of Proteome Research · 2017
| Date | 2017-01-23 |
| Type | peer-reviewed |
| Venue | Journal of Proteome Research |
| Publisher | ACS |
| Contribution | algorithm |
| DOI | 10.1021/acs.jproteome.6b00716 |
| Citations (OpenAlex) | 36 |
| Venue 2-year citedness | 3.48 |
Abstract
De novo peptide sequencing has improved remarkably, but sequencing full-length peptides with unexpected modifications is still a challenging problem. Here we present an open de novo sequencing tool, Open-pNovo, for de novo sequencing of peptides with arbitrary types of modifications. Although the search space increases by ∼300 times, Open-pNovo is close to or even ∼10-times faster than the other three proposed algorithms. Furthermore, considering top-1 candidates on three MS/MS data sets, Open-pNovo can recall over 90% of the results obtained by any one traditional algorithm and report 5-87% more peptides, including 14-250% more modified peptides. On a high-quality simulated data set, ∼85% peptides with arbitrary modifications can be recalled by Open-pNovo, while hardly any results can be recalled by others. In summary, Open-pNovo is an excellent tool for open de novo sequencing and has great potential for discovering unexpected modifications in the real biological applications.
Methods and tools
- Open-pNovo: pNovo with thousands of PTMs
Cites (17)
- UniNovo: a universal tool for de novo peptide sequencing (2013) crossref
- pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (2013) crossref
- PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012) crossref
- De Novo Sequencing and Homology Searching (2012) crossref
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring (2008) crossref
- De Novo Peptide Sequencing and Identification with Precision 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
- Algorithms for de novo peptide sequencing using tandem mass spectrometry (2004) crossref
- GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model (2003) crossref
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry (2001) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) crossref
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) crossref
Cited by (8)
- A large-scale unified deep learning model for peptide mass spectrum interpretation trained on multimodal data (2026) crossref
- pUniFind: a unified large pre-trained deep learning model pushing the limit of mass spectra interpretation (2025) semanticscholar
- Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023) both
- Highly Robust de Novo Full-Length Protein Sequencing (2021) both
- De novo sequencing of proteins by mass spectrometry (2020) both
- pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework (2019) both
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization (2017) crossref