NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing
peer-reviewed · Analytical Chemistry · 2005
peer-reviewed · Analytical Chemistry · 2005. Bernd Fischer et al. De novo sequencing of peptides poses one of the most challenging tasks in data analysis for proteome…
| Date | 2005-11-15 |
| Type | peer-reviewed |
| Venue | Analytical Chemistry |
| Publisher | American Chemical Society |
| Contribution | algorithm |
| DOI | 10.1021/ac0508853 |
| Citations (OpenAlex) | 192 |
| Venue 2-year citedness | 6.29 |
Abstract
De novo sequencing of peptides poses one of the most challenging tasks in data analysis for proteome research. In this paper, a generative hidden Markov model (HMM) of mass spectra for de novo peptide sequencing which constitutes a novel view on how to solve this problem in a Bayesian framework is proposed. Further extensions of the model structure to a graphical model and a factorial HMM to substantially improve the peptide identification results are demonstrated. Inference with the graphical model for de novo peptide sequencing estimates posterior probabilities for amino acids rather than scores for single symbols in the sequence. Our model outperforms state-of-the-art methods for de novo peptide sequencing on a large test set of spectra.
Methods and tools
- NovoHMM: Generative HMM scoring
Cites (3)
Cited by (40)
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- Deep Learning Methods for De Novo Peptide Sequencing (2024) crossref
- Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo (2024) both
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2024) both
- NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics (2024) semanticscholar
- AdaNovo: Adaptive De Novo Peptide Sequencing with Conditional Mutual Information (2024) semanticscholar
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2024) crossref
- Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023) both
- SeqNovo: De Novo Peptide Sequencing Prediction in IoMT via Seq2Seq (2023) crossref
- Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
- Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics (2023) both
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2023) crossref
- De novo mass spectrometry peptide sequencing with a transformer model (2022) semanticscholar
- DePS: An improved deep learning model for de novo peptide sequencing (2022) semanticscholar
- De novo mass spectrometry peptide sequencing with a transformer model (2022) both
- Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra (2021) both
- De novo sequencing of proteins by mass spectrometry (2020) crossref
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- De novo peptide sequencing by deep learning (2017) crossref
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications (2017) crossref
- Peptide de novo sequencing of mixture tandem mass spectra (2016) both
- UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry (2016) both
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) both
- 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) both
- Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem (2012) both
- De Novo Sequencing and Homology Searching (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR (2010) semanticscholar
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) crossref
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009) both
- 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) crossref
- De Novo Peptide Identification via Tandem Mass Spectrometry and Integer Linear Optimization (2007) crossref
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) crossref
- A mixed-integer optimization framework for de novo peptide identification (2007) crossref
- Performance Evaluation of Existing De Novo Sequencing Algorithms (2006) crossref