Utrecht University
Utrecht, Netherlands · 50 authors
Utrecht University (Utrecht, Netherlands): 50 authors and 34 papers in the de novo peptide sequencing catalog.
Departments
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research
- Department of Pharmaceutical Sciences
Papers (34)
- Reference-free protein sequencing by consensus assembly of redundant de novo peptide reads (2026, bioRxiv)
- Deep coverage and extended sequence reads obtained with a single archaeal protease expedite de novo protein sequencing by mass spectrometry (2026, Cell Systems)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2025, Cell Systems)
- Structural Basis for Postfusion-Specific Binding to the Respiratory Syncytial Virus F Protein by the Canonical Antigenic Site I Antibody 131–2a (2025, ACS Infectious Diseases)
- Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry (2025, eLife)
- Interferon-α promotes HLA-B-restricted presentation of conventional and alternative antigens in human pancreatic β-cells (2025, Nature Communications)
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2024, bioRxiv)
- A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics (2024, Journal of Proteome Research)
- Reverse-engineering the anti-MUC1 antibody 139H2 by mass spectrometry–based de novo sequencing (2024, Life Science Alliance)
- De novo antibody sequencing based on mass spectrometry (2024)
- MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer (2024, Nature Communications)
- Into the Dark Serum Proteome: Personalized Features of IgG1 and IgA1 Repertoires in Severe COVID-19 Patients (2024, Molecular & Cellular Proteomics)
- Direct Mass Spectrometry-Based Detection and Antibody Sequencing of Monoclonal Gammopathy of Undetermined Significance from Patient Serum: A Case Study (2023, Journal of Proteome Research)
- Reverse engineering the anti-MUC1 hybridoma antibody 139H2 by mass spectrometry-based de novo sequencing (2023, bioRxiv)
- A perspective toward mass spectrometry-based de novo sequencing of endogenous antibodies (2022, mAbs)
- No patient is the same; lessons learned from antibody repertoire profiling in hospitalized severe COVID-19 patients (2022, medRxiv)
- Probing highly polymorphic proteins by mass spectrometry (2022)
- MARS: Improved De Novo Peptide Candidate Selection for Non-Canonical Antigen Target Discovery in Cancer (2022, Research Square)
- Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling (2022, Analytical Chemistry)
- Template-based assembly of proteomic short reads for de novo antibody sequencing and repertoire profiling (2022, bioRxiv)
- Human plasma IgG1 repertoires are simple, unique, and dynamic (2021, Cell Systems)
- The lysosomal endopeptidases Cathepsin D and L are selective and effective proteases for the middle‐down characterization of antibodies (2021, The FEBS Journal)
- The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires (2021, Molecular & Cellular Proteomics)
- Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme (2021, Journal of Proteome Research)
- Mass spectrometry-based de novo sequencing of the anti-FLAG-M2 antibody using multiple proteases and a dual fragmentation scheme (2021, bioRxiv)
- Comprehensive identification of native medium-sized and short bioactive peptides in sea bass muscle (2020, Food Chemistry)
- Selectivity over coverage in de novo sequencing of IgGs (2020, Chemical Science)
- Elucidation of the Signatures of Proteasome-Catalyzed Peptide Splicing (2020, Frontiers in Immunology)
- De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri (2015, EuPA Open Proteomics)
- Database independent proteomics analysis of the ostrich and human proteome (2012, Proceedings of the National Academy of Sciences)
- Lys-N: A versatile enzyme for proteomics (2010)
- Dimethyl isotope labeling assisted de novo peptide sequencing (2010, Journal of the American Society for Mass Spectrometry)
- LysNDeNovo: An algorithm enabling de novo sequencing of Lys‐N generated peptides fragmented by electron transfer dissociation (2010, PROTEOMICS)
- Straightforward and de Novo Peptide Sequencing by MALDI-MS/MS Using a Lys-N Metalloendopeptidase (2009, Molecular & Cellular Proteomics)