Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review
peer-reviewed · Analytica Chimica Acta · 2023
peer-reviewed · Analytica Chimica Acta · 2023. Cheuk Chi A. Ng et al.
| Date | 2023-08-01 |
| Type | peer-reviewed |
| Venue | Analytica Chimica Acta |
| Publisher | Elsevier BV |
| Contribution | review |
| DOI | 10.1016/j.aca.2023.341330 |
| Citations (OpenAlex) | 48 |
| Venue 2-year citedness | 4.96 |
Methods and tools
- Algorithms for de-novo sequencing of peptides (comprehensive survey): Analytica Chimica Acta review of de novo peptide sequencing algorithms for tandem mass spectrometry.
Cites (39)
- Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics (2023) crossref
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) crossref
- Direct Identification of Urinary Tract Pathogens by MALDI-TOF/TOF Analysis and De Novo Peptide Sequencing (2022) crossref
- De novo mass spectrometry peptide sequencing with a transformer model (2022) crossref
- DePS: An improved deep learning model for de novo peptide sequencing (2022) crossref
- PepNet: A Fully Convolutional Neural Network for De novo Peptide Sequencing (2022) crossref
- Highly Robust de Novo Full-Length Protein Sequencing (2021) crossref
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- De novo sequencing of proteins by mass spectrometry (2020) crossref
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
- De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments (2020) crossref
- Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework (2019) crossref
- pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework (2019) crossref
- DeepNovoV2: Better de novo peptide sequencing with deep learning (2019) crossref
- Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry (2018) crossref
- 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
- 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
- UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry (2016) crossref
- Recent Developments in Computational Methods for De Novo Peptide Sequencing from Tandem Mass Spectrometry (MS/MS) (2015) crossref
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) crossref
- Lessons in de novo peptide sequencing by tandem mass spectrometry (2015) crossref
- 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
- De Novo Sequencing and Homology Searching (2012) crossref
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) crossref
- De novo sequencing of peptides by MS/MS (2010) crossref
- De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation (2009) crossref
- DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring (2008) crossref
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) crossref
- NovoHMM: A Hidden Markov Model for de Novo Peptide Sequencing (2005) crossref
- An effective algorithm for peptide de novo sequencing from MS/MS spectra (2005) crossref
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) 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
- Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (2000) crossref
- De novo peptide sequencing via tandem mass spectrometry (1999) crossref
Cited by (9)
- Improvements to Casanovo, a Deep Learning De Novo Peptide Sequencer (2025) crossref
- Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (2025) semanticscholar
- Framework for de novo sequencing of peptide mixtures via network analysis and two-dimensional tandem mass spectrometry (2025) crossref
- Improvements to CasaNovo, a deep learning de novo peptide sequencer (2025) crossref
- Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing (2025) semanticscholar
- De Novo Peptide Sequencing for Data-independent Acquisition (DIA) Using Deep Learning (2025) crossref
- DiNovo: high-coverage, high-confidence de novo peptide sequencing using mirror proteases and deep learning (2025) crossref
- Deep Learning Methods for De Novo Peptide Sequencing (2024) crossref
- A transformer model for de novo sequencing of data independent acquisition mass spectrometry data (2024) crossref