A Hidden Markov Model for de Novo Peptide Sequencing
ML conference · NIPS 2004 · 2004
ML conference · NIPS 2004 · 2004. Bernd Fischer et al. De novo sequencing of peptides poses one of the most challenging tasks in data analysis for proteome…
| Date | 2004-12-13 |
| Type | ML conference |
| Venue | NIPS 2004 |
| Publisher | MIT Press |
| Contribution | algorithm |
| Link | https://papers.nips.cc/paper_files/paper/2004/hash/5ac8bb8a7d745102a978c5f8ccdb61b8-Abstract.html |
| Citations (OpenAlex) | 192 |
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
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- Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023) semanticscholar
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- PRESnovo: Prescreening Prior to de novo Sequencing to Improve Accuracy and Sensitivity of Neuropeptide Identification (2020) semanticscholar
- Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics (2019) semanticscholar
- Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries (2017) semanticscholar
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- The spectral networks paradigm in high throughput mass spectrometry (2012) semanticscholar
- Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem (2012) semanticscholar
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- Homology‐Driven Proteomics of Dinoflagellates with Unsequenced Genomes Using MALDI‐TOF/TOF and Automated De Novo Sequencing (2011) semanticscholar
- Acetylating Tryptic Peptides Enhances b Ion Intensity in MALDI TOF/TOF: Implications in Peptide Sequencing and Identification of Proteins in an Antarctic Bacterium Pseudomonas Syringae (2010) semanticscholar
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- Multi-spectra peptide sequencing and its applications to multistage mass spectrometry (2008) semanticscholar
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- Spectral Networks: A New Approach to De Novo Discovery of Protein Sequences and Posttranslational Modifications (2007) semanticscholar
- Probabilistic De Novo Peptide Sequencing with Doubly Charged Ions (2006) crossref