University of Waterloo

Waterloo, Canada · 23 authors

University of Waterloo (Waterloo, Canada): 23 authors and 73 papers in the de novo peptide sequencing catalog.

Departments

David R. Cheriton School of Computer Science
Department of Electrical and Computer Engineering
Department of Statistics and Actuarial Science
Department of Systems Design Engineering
School of Computer Science

Papers (73)

High-accuracy glycan de novo prediction for N- and O-linked glycopeptides across multiple fragmentation techniques (2026, Nature Communications)
AI proteomics: from protein identification to virtual cells (2026, Nature Methods)
Zero-shot de novo peptide sequencing with open posttranslational modification discovery (2026, Nature Biotechnology)
Mass spectrometry-based de novo sequencing reveals non-canonical neoantigens with antitumor efficacy in hepatocellular carcinoma (2026, JHEP Reports)
A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026, Nature Methods (Registered Report))
Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Middle–Down, and De Novo Bottom–Up Mass Spectrometry (2025, Molecular & Cellular Proteomics)
Identification of broadly inhibitory anti-PfEMP1 antibodies by mass spectrometry sequencing of plasma IgG from a malaria-exposed child (2025, Proceedings of the National Academy of Sciences)
Advancing Proteomic Analyses with Graph-Based Deep Learning: Protein Inference and DIA De Novo Peptide Sequencing (2025)
Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases (2025, Nature Communications)
Diffusion Decoding for Peptide De Novo Sequencing (2025, arXiv)
Zero-Shot De Novo Peptide Sequencing with Open Post-Translational Modification Discovery (2025, Research Square)
Do-It-Yourself De Novo Antibody Sequencing Workflow that Achieves Complete Accuracy of the Variable Regions (2025, Journal of Proteome Research)
De Novo sequencing-assisted homology search for DIA data analysis enables low abundance peptide variants discovery (2025, bioRxiv)
Generative AI Models for the Protein Scaffold Filling Problem (2025, Journal of Computational Biology)
Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing (2024, arXiv)
1086 Sequencing antibodies from de novo to identify functional and neutralizing antibodies in human plasma after SARS-CoV-2 vaccination (2024, Regular and Young Investigator Award Abstracts)
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing (2024, Molecular & Cellular Proteomics)
Enhancing De Novo Protein Sequencing through the C-Terminal Labeling Strategy: Resolving Isobaric Ambiguities by Electron-Transfer/Higher Energy Collision Dissociation (EThcD) (2024, Analytical Chemistry)
De novo protein sequencing of antibodies for identification of neutralizing antibodies in human plasma post SARS-CoV-2 vaccination (2024, Nature Communications)
Ultra-sensitivity metaproteomics redefines the gut “dark metaproteome”, uncovering host-microbiome interactions and drug targets in intestinal inflammatory diseases (2024, bioRxiv)
NovoBoard: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing (2024, bioRxiv)
de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination (2024, bioRxiv)
A complete mass spectrometry-based immunopeptidomics pipeline for neoantigen identification and validation (2023, Research Square)
Mitigating the missing-fragmentation problem in de novo peptide sequencing with a two-stage graph-based deep learning model (2023, Nature Machine Intelligence)
Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics (2023, Nature Communications)
PaSER Novor: Real-time de novo sequencing for 4D-Proteomics applications (2023)
Deep Learning Approaches for the Protein Scaffold Filling Problem (2022, 2022 IEEE 34th International Conference on Tools with Artificial Intelligence (ICTAI))
Discovering and Validating Neoantigens by Mass Spectrometry-based Immunopeptidomics and Deep Learning (2022, bioRxiv)
A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics (2022, Nature Communications)
A Personalized Mass Spectrometry–Based Assay to Monitor M-Protein in Patients with Multiple Myeloma (EasyM) (2021, Clinical Cancer Research)
Mass Spectrometry Provides a Highly Sensitive Noninvasive Means of Sequencing and Tracking M-Protein in the Blood of Multiple Myeloma Patients (2021, Journal of Proteome Research)
Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices (2021, Nature Machine Intelligence)
Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2020, Nature Machine Intelligence)
Peptide Sequencing with Deep Learning (2020)
Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines (2019, bioRxiv)
DeepNovoV2: Better de novo peptide sequencing with deep learning (2019, arXiv)
Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing (2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics)
Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry (2018, Nature Methods)
De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods (2017, PROTEOMICS)
Protein identification with deep learning: from abc to xyz (2017, arXiv)
Discovery of New Features for Peptide Sequencing with Mass Spectrometry (2017)
De novo peptide sequencing by deep learning (2017, Proceedings of the National Academy of Sciences)
Filling a Protein Scaffold With a Reference (2017, IEEE Transactions on NanoBioscience)
An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra (2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics)
De novo Peptide Sequencing (2016, Proteome Informatics)
Top-down analysis of protein samples by de novo sequencing techniques (2016, Bioinformatics)
Complete De Novo Assembly of Monoclonal Antibody Sequences (2016, Scientific Reports)
Filling a Protein Scaffold with a Reference (2016, Lecture Notes in Computer Science)
De Novo Sequencing Assisted Approach for Characterizing Mixture MS/MS Spectra (2016, IEEE Transactions on NanoBioscience)
De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra (2015, Journal of Proteome Research)
Novor: Real-Time Peptide de Novo Sequencing Software (2015, Journal of the American Society for Mass Spectrometry)
An Approach for Matching Mixture MS/MS Spectra with a Pair of Peptide Sequences in a Protein Database (2015, Lecture Notes in Computer Science)
De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014, Journal of Proteome Research)
An Effective Algorithm for Peptide de novo Sequencing from Mixture MS/MS Spectra (2014, Lecture Notes in Computer Science)
DE NOVO SEQUENCING WITH LIMITED NUMBER OF POST-TRANSLATIONAL MODIFICATIONS PER PEPTIDE (2013, Journal of Bioinformatics and Computational Biology)
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012, Molecular & Cellular Proteomics)
De Novo Sequencing and Homology Searching (2012, Molecular & Cellular Proteomics)
Integrating de Novo Sequencing and Database Search for Peptide Identification (2012, Europe PMC (PubMed Central))
SPIDER: Reconstructive Protein Homology Search with De Novo Sequencing Tags (2011)
ADEPTS: Advanced peptide de novo sequencing with a pair of tandem mass spectra (2010, Journal of Bioinformatics and Computational Biology)
An Automata Approach to Match Gapped Sequence Tags Against Protein Database (2010, Lecture Notes in Computer Science)
Better score function for peptide identification with ETD MS/MS spectra (2010, BMC Bioinformatics)
De Novo Sequencing Methods in Proteomics (2009, Methods in Molecular Biology)
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy (2009, Bioinformatics)
De Novo Interpretation of Tandem Mass Spectra (2009, Current Protocols in Bioinformatics)
Peptide De Novo Sequencing with MS/MS (2008, Encyclopedia of Algorithms)
Improving de novo sequencing accuracy for Ion Trap data in PEAKS software (2007)
Complexity and scoring function of MS/MS peptide de novo sequencing (2006, Computational Systems Bioinformatics)
AN AUTOMATA APPROACH TO MATCH GAPPED SEQUENCE TAGS AGAINST PROTEIN DATABASE (2005, International Journal of Foundations of Computer Science)
SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005, Journal of Bioinformatics and Computational Biology)
An effective algorithm for peptide de novo sequencing from MS/MS spectra (2005, Journal of Computer and System Sciences)
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003, Rapid Communications in Mass Spectrometry)
An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum (2003, Lecture Notes in Computer Science)

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