Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices

peer-reviewed · Nature Machine Intelligence · 2021

peer-reviewed · Nature Machine Intelligence · 2021. Rui Qiao et al.

Date	2021-03-18
Type	peer-reviewed
Venue	Nature Machine Intelligence
Publisher	Nature Machine Intelligence
Contribution	algorithm
DOI	10.1038/s42256-021-00304-3
Citations (OpenAlex)	103
Venue 2-year citedness	19.94

Authors

Methods and tools

PointNovo: Point-set network

Cites (11)

Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (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
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry (2018) crossref
De novo peptide sequencing by deep learning (2017) crossref
Novor: Real-Time Peptide de Novo Sequencing Software (2015) 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
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

Cited by (54)

A large-scale unified deep learning model for peptide mass spectrum interpretation trained on multimodal data (2026) crossref
Zero-shot de novo peptide sequencing with open posttranslational modification discovery (2026) crossref
Regressor-guided Diffusion Model for De Novo Peptide Sequencing with Explicit Mass Control (2026) semanticscholar
AbNovoBench: a resource and benchmarking platform for monoclonal antibody de novo sequencing (2026) crossref
Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (2025) semanticscholar
pUniFind: a unified large pre-trained deep learning model pushing the limit of mass spectra interpretation (2025) semanticscholar
MassNet: billion-scale AI-friendly mass spectral corpus enables robust de novo peptide sequencing (2025) crossref
Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing (2025) semanticscholar
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra (2025) both
Latent Imputation before Prediction: A New Computational Paradigm for De Novo Peptide Sequencing (2025) semanticscholar
PSMtags improve peptide sequencing and throughput in sensitive proteomics (2025) crossref
De Novo Peptide Sequencing for Data-independent Acquisition (DIA) Using Deep Learning (2025) crossref
InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025) both
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra (2025) both
DiNovo: high-coverage, high-confidence de novo peptide sequencing using mirror proteases and deep learning (2025) crossref
PepGo: a deep learning and tree search-based model for de novo peptide sequencing (2025) semanticscholar
A transformer-based semi-autoregressive framework for high-speed and accurate de novo peptide sequencing (2025) both
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing (2025) crossref
π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing (2025) both
Deep Learning Methods for De Novo Peptide Sequencing (2024) crossref
Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing (2024) semanticscholar
A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models (2024) both
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing (2024) crossref
Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo (2024) both
Accounting for Digestion Enzyme Bias in Casanovo (2024) crossref
Transforming de novo peptide sequencing by explainable AI (2024) crossref
Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2024) both
PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models (2024) crossref
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
NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of 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
Introducing π-HelixNovo for practical large-scale de novo peptide sequencing (2024) crossref
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
Multi-Modal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O (2023) crossref
Accurate de novo peptide sequencing using fully convolutional neural networks (2023) both
Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023) both
De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023) both
Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
Introducing PandaNovo for practical large-scale de novo peptide sequencing (2023) both
Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics (2023) both
BiATNovo: A Self-Attention based Bidirectional Peptide Sequencing Method (2023) both
PGPointNovo: an efficient neural network-based tool for parallel de novo peptide sequencing (2023) both
Denovo-GCN: De Novo Peptide Sequencing by Graph Convolutional Neural Networks (2023) both
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) both
Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2023) crossref
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
DPST: De Novo Peptide Sequencing with Amino-Acid-Aware Transformers (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

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