University of California San Diego
San Diego, USA, La Jolla, USA, La Jolla · 41 authors
University of California San Diego (San Diego, USA, La Jolla, USA, La Jolla): 41 authors and 88 papers in the de novo peptide sequencing catalog.
Departments
- Bioinformatics Program
- California Institute for Telecommunications and Information Technology
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering
- Center for Microbiome Innovation
- Department of Bioengineering and Computer Science Department
- Department of Computer Science and Engineering
- Department of Electrical and Computer Engineering and Department of Computer Science and Engineering
- Department of Pharmacology
- Integrated Space Stem Cell Orbital Research (ISSCOR) Center
- Skaggs School of Pharmacy and Pharmaceutical Sciences
Papers (88)
- AI proteomics: from protein identification to virtual cells (2026, Nature Methods)
- CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo (2026, bioRxiv)
- A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026, Nature Methods (Registered Report))
- Improvements to Casanovo, a Deep Learning De Novo Peptide Sequencer (2025, Journal of Proteome Research)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2025, Cell Systems)
- SequenceAssembler: A tool for protein sequence assembly from mass spectrometry data (2025, Journal of Proteomics)
- Improvements to CasaNovo, a deep learning de novo peptide sequencer (2025, bioRxiv)
- Enamel proteins reveal biological sex and genetic variability in southern African Paranthropus (2025, Science)
- Foundation model for mass spectrometry proteomics (2025, arXiv)
- Deep Learning Methods for De Novo Peptide Sequencing (2024, Mass Spectrometry Reviews)
- Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins (2024, Peer Community Journal)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2024, bioRxiv)
- Accounting for Digestion Enzyme Bias in Casanovo (2024, Journal of Proteome Research)
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2024, Nature Communications)
- Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins (2023, bioRxiv)
- Accurate de novo peptide sequencing using fully convolutional neural networks (2023, Nature Communications)
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2023, bioRxiv)
- De novo sequencing and construction of a unique antibody for the recognition of alternative conformations of cytochrome c in cells (2022, Proceedings of the National Academy of Sciences)
- De novo mass spectrometry peptide sequencing with a transformer model (2022, ICML 2022)
- PepNet: A Fully Convolutional Neural Network for De novo Peptide Sequencing (2022, Research Square)
- De novo mass spectrometry peptide sequencing with a transformer model (2022, bioRxiv)
- ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping (2020, Molecular & Cellular Proteomics)
- De novo sequencing of proteins by mass spectrometry (2020, Expert Review of Proteomics)
- The dental proteome of Homo antecessor (2020, Nature)
- De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments (2020, Cell Systems)
- Enamel proteome shows that Gigantopithecus was an early diverging pongine (2019, Nature)
- 2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample (2019, Journal of Proteome Research)
- Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny (2019, Nature)
- Quick and clean: Cracking sentences encoded in E. coli by LC–MS/MS, de novo sequencing, and dictionary search (2019, EuPA Open Proteomics)
- De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments (2019, bioRxiv)
- Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry (2018, Lecture Notes in Computer Science)
- Antibody de novo Sequencing (2017, Analytical Characterization of Biotherapeutics)
- Data from proteome analysis of Lasiodiplodia theobromae (Botryosphaeriaceae) (2017, Data in Brief)
- A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom (2017, Scientific Data)
- Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae) (2017, Biochimie Open)
- De Novo MS/MS Sequencing of Native Human Antibodies (2017, Journal of Proteome Research)
- Protein sequences bound to mineral surfaces persist into deep time (2016, eLife)
- Top-down analysis of protein samples by de novo sequencing techniques (2016, Bioinformatics)
- De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra (2015, Journal of Proteome Research)
- Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results (2015, Current Protocols in Bioinformatics)
- PepExplorer: A Similarity-driven Tool for Analyzing de Novo Sequencing Results (2014, Molecular & Cellular Proteomics)
- De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014, Journal of Proteome Research)
- Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo‐peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms (2014, Rapid Communications in Mass Spectrometry)
- Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (2013, Molecular & Cellular Proteomics)
- UniNovo: a universal tool for de novo peptide sequencing (2013, Bioinformatics)
- Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013, Journal of Proteome Research)
- Shotgun Protein Sequencing with Meta-contig Assembly (2012, Molecular & Cellular Proteomics)
- The spectral networks paradigm in high throughput mass spectrometry (2012, Molecular BioSystems)
- Investigation of VUV photodissociation propensities using peptide libraries (2011, International Journal of Mass Spectrometry)
- A mass spectrometry–guided genome mining approach for natural product peptidogenomics (2011, Nature Chemical Biology)
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011, Journal of Computational Biology)
- De novo Sequencing of Proteins With Mass Spectrometry Using the Differential Scanning Technique (2011, Proteome and Protein Analysis)
- Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2011, Molecular & Cellular Proteomics)
- Multiplex De Novo Sequencing of Peptide Antibiotics (2011, Lecture Notes in Computer Science)
- Resurrection of a clinical antibody: Template proteogenomic de novo proteomic sequencing and reverse engineering of an anti‐lymphotoxin‐α antibody (2011, PROTEOMICS)
- Template Proteogenomics: Sequencing Whole Proteins Using an Imperfect Database (2010, Molecular & Cellular Proteomics)
- Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2010, Lecture Notes in Computer Science)
- Dereplication and de novo sequencing of nonribosomal peptides (2009, Nature Methods)
- Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009, Molecular & Cellular Proteomics)
- A Ranking-Based Scoring Function for Peptide-Spectrum Matches (2009, Journal of Proteome Research)
- Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009, Molecular & Cellular Proteomics)
- How much peptide sequence information is contained in ion trap tandem mass spectra? (2008, Journal of the American Society for Mass Spectrometry)
- Automated de novo protein sequencing of monoclonal antibodies (2008, Nature Biotechnology)
- Simplified validation of borderline hits of database searches (2008, PROTEOMICS)
- Multi-spectra peptide sequencing and its applications to multistage mass spectrometry (2008, Bioinformatics)
- De Novo Sequencing of Nonribosomal Peptides (2008, Lecture Notes in Computer Science)
- Sequence similarity‐driven proteomics in organisms with unknown genomes by LC‐MS/MS and automated de novo sequencing (2007, PROTEOMICS)
- Shotgun Protein Sequencing: Assembly of Peptide Tandem Mass Spectra from Mixtures of Modified Proteins (2007, Molecular & Cellular Proteomics)
- Spectral Networks: A New Approach to De Novo Discovery of Protein Sequences and Posttranslational Modifications (2007, BioTechniques)
- Protein identification by spectral networks analysis (2007, Proceedings of the National Academy of Sciences)
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007, Journal of Proteome Research)
- MODELING AND CHARACTERIZATION OF MULTI-CHARGE MASS SPECTRA FOR PEPTIDE SEQUENCING (2006, Journal of Bioinformatics and Computational Biology)
- Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches (2006, Journal of Proteome Research)
- CHARACTERIZATION OF MULTI-CHARGE MASS SPECTRA FOR PEPTIDE SEQUENCING (2005, Proceedings of the 4th Asia-Pacific Bioinformatics Conference)
- Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry (2005, Journal of Proteome Research)
- InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra (2005, Analytical Chemistry)
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005, Analytical Chemistry)
- Shotgun Protein Sequencing by Tandem Mass Spectra Assembly (2004, Analytical Chemistry)
- The Power and the Limitations of Cross-Species Protein Identification by Mass Spectrometry-driven Sequence Similarity Searches (2004, Molecular & Cellular Proteomics)
- De novo sequencing of antimicrobial peptides isolated from the venom glands of the wolf spider Lycosa singoriensis (2004, Journal of Mass Spectrometry)
- “De Novo” Sequencing of Peptides Recovered from In-Gel Digested Proteins by Nanoelectrospray Tandem Mass Spectrometry (2003, Molecular Biotechnology)
- De Novo Peptide Sequencing by Nanoelectrospray Tandem Mass Spectrometry Using Triple Quadrupole and Quadrupole/Time-of-Flight Instruments (2003, Mass Spectrometry of Proteins and Peptides)
- On de novo interpretation of tandem mass spectra for peptide identification (2003, Proceedings of the seventh annual international conference on Research in computational molecular biology)
- MultiTag: Multiple Error-Tolerant Sequence Tag Search for the Sequence-Similarity Identification of Proteins by Mass Spectrometry (2003, Analytical Chemistry)
- Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching (2001, Analytical Chemistry)
- De novo peptide sequencing via tandem mass spectrometry (1999, Journal of Computational Biology)
- Rapid de novo peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer (1997, Rapid Communications in Mass Spectrometry)
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994, Analytical Chemistry)