Improvements to Casanovo, a Deep Learning De Novo Peptide Sequencer

peer-reviewed · Journal of Proteome Research · 2025

peer-reviewed · Journal of Proteome Research · 2025. Gwenneth Straub et al. Casanovo is a state-of-the-art deep learning model for de novo peptide sequencing from mass spectrometry and…
Date 2025-12-30
Type peer-reviewed
Venue Journal of Proteome Research
Publisher American Chemical Society (ACS)
Contribution algorithm
DOI 10.1021/acs.jproteome.5c00706
Citations (OpenAlex) 6
Venue 2-year citedness 3.83

Preprint version: Improvements to CasaNovo, a deep learning de novo peptide sequencer (2025-07-25, bioRxiv)

Abstract

Casanovo is a state-of-the-art deep learning model for de novo peptide sequencing from mass spectrometry and proteomics data. Here, we report on a series of enhancements to Casanovo, aimed at improving the interpretability of the scores assigned to predicted peptides, generalizing the software for use in database searches, speeding up training and prediction runtimes, and providing workflows and visualization tools to facilitate adoption of Casanovo and interpretation of its results. Our goal is to make Casanovo accurate and easy to use for applications such as metaproteomics, antibody sequencing, immunopeptidomics, and the discovery of novel peptide sequences in standard proteomics analyses. Casanovo is available as open source at https://github.com/Noble-Lab/casanovo.

Authors

  1. Gwenneth Straub · University of Washington
  2. Varun Ananth · University of Washington
  3. William E. Fondrie · Talus Bioscience
  4. Chris Hsu · University of Washington
  5. Daniela Klaproth-Andrade · Technical University of Munich
  6. Marina Pominova · University of Antwerp
  7. Michael Riffle · University of Washington
  8. Justin Sanders · University of Washington
  9. Bo Wen · Baylor College of Medicine, University of Washington
  10. Lingwen Xu · University of Washington
  11. Melih Yilmaz · University of Washington
  12. Michael J. MacCoss · University of Washington
  13. Sewoong Oh · University of Washington
  14. Wout Bittremieux · Biomedical Informatics Research Center Antwerp, Indiana University, University of Antwerp, University of California San Diego, University of Washington
  15. William Stafford Noble · University of Washington

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