Novor: Real-Time Peptide de Novo Sequencing Software
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2015
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2015. Bin Ma. De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass…
| Date | 2015-06-30 |
| Type | peer-reviewed |
| Venue | Journal of the American Society for Mass Spectrometry |
| Publisher | Springer |
| Contribution | algorithm |
| DOI | 10.1007/s13361-015-1204-0 |
| Citations (OpenAlex) | 279 |
| Venue 2-year citedness | 2.58 |
Abstract
De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today’s peptide de novo sequencing analyses. To improve the accuracy, Novor’s scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today’s mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data. Graphical Abstract ᅟ.
Methods and tools
- Novor: Real-time decision-tree scoring
Cites (16)
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- Learning Fragmentation Physics or Exploiting Sequence Priors? Benchmarking Bias in Deep Learning Models for De Novo Peptide Sequencing (2026) both
- DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics (2026) crossref
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- NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics (2024) semanticscholar
- π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing (2024) crossref
- AdaNovo: Adaptive De Novo Peptide Sequencing with Conditional Mutual Information (2024) semanticscholar
- Bidirectional de novo peptide sequencing using a transformer model (2024) both
- Transformer-Based De Novo Peptide Sequencing for Data-Independent Acquisition Mass Spectrometry (2024) semanticscholar
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2024) crossref
- Transformer-Based De Novo Peptide Sequencing for Data-Independent Acquisition Mass Spectrometry (2023) crossref
- Accurate de novo peptide sequencing using fully convolutional neural networks (2023) both
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- Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
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- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) both
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- 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
- Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics (2022) both
- Metaproteomic Characterization of Forensic Samples (2022) crossref
- 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
- Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices (2021) crossref
- De novo sequencing of proteins by mass spectrometry (2020) both
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
- Deep Learning in Proteomics (2020) both
- Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework (2019) both
- pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework (2019) both
- GA-Novo: De Novo Peptide Sequencing via Tandem Mass Spectrometry Using Genetic Algorithm (2019) both
- Postnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing (2018) crossref
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines (2018) crossref
- pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization (2017) crossref
- De novo peptide sequencing by deep learning (2017) crossref
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- Comprehensive de Novo Peptide Sequencing from MS/MS Pairs Generated through Complementary Collision Induced Dissociation and 351 nm Ultraviolet Photodissociation (2017) crossref
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