How to Cite Casanovo

How to Cite Casanovo#

When using Casanovo in your research, please cite the relevant scientific publications to acknowledge the work and contributions behind the tool. Below, you will find detailed information on how to cite Casanovo, including citations for its various versions and functionalities.

For general use of Casanovo, please cite the following paper:

Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo mass spectrometry peptide sequencing with a transformer model. in Proceedings of the 39th International Conference on Machine Learning - ICML ‘22 vol. 162 25514–25522 (PMLR, 2022). https://proceedings.mlr.press/v162/yilmaz22a.html

In addition, you may wish to cite one or more of these additional publications, depending on relevance to your work.

  • For improved performance of Casanovo by training on the MassIVE-KB data and applications in immunopeptidomics, metaproteomics, and the dark human proteome (Casanovo v4.x):
    Yilmaz, M., et al. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in Nature Communications 15, 6427 (2024). doi:10.1038/s41467-024-49731-x

  • For work involving Casanovo’s enhanced performance on tryptic and non-tryptic data (Casanovo v4.2.x):
    Melendez, C., et al. Accounting for digestion enzyme bias in Casanovo. in Journal of Proteome Research 23, 4761–4769 (2024). doi:10.1021/acs.jproteome.4c00422

  • For using Casanovo as a learned score function for sequence database searching (Casanovo-DB):
    Ananth, V., et al. A learned score function improves the power of mass spectrometry database search. in Bioinformatics 40, i410–i417 (2024). doi:10.1093/bioinformatics/btae218

  • For performance and usability improvements to Casanovo (Casanovo v5.x):
    Straub, G., et al. Improvements to Casanovo, a deep learning de novo peptide sequencer. in bioRxiv (2025). doi:10.1101/2025.07.25.666826

Notes for Citation#

  • Always ensure you are citing the correct version or functionality of Casanovo relevant to your use case.

  • If you have questions about how to cite Casanovo in specific scenarios, feel free to reach out to the Casanovo community or maintainers.

By citing Casanovo appropriately, you help support the ongoing development and innovation of this open-source tool. Thank you for contributing to the community.

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