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How to cite?

InstaNovo & InstaNovo+

If you use InstaNovo or InstaNovo+ in your research, please cite our publication in Nature Machine Intelligence: InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments:

@article{eloff_kalogeropoulos_2025_instanovo,
        title        = {InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale
                        proteomics experiments},
        author       = {Eloff, Kevin and Kalogeropoulos, Konstantinos and Mabona, Amandla and Morell,
                        Oliver and Catzel, Rachel and Rivera-de-Torre, Esperanza and Berg Jespersen,
                        Jakob and Williams, Wesley and van Beljouw, Sam P. B. and Skwark, Marcin J.
                        and Laustsen, Andreas Hougaard and Brouns, Stan J. J. and Ljungars,
                        Anne and Schoof, Erwin M. and Van Goey, Jeroen and auf dem Keller, Ulrich and
                        Beguir, Karim and Lopez Carranza, Nicolas and Jenkins, Timothy P.},
        year         = 2025,
        month        = {Mar},
        day          = 31,
        journal      = {Nature Machine Intelligence},
        doi          = {10.1038/s42256-025-01019-5},
        issn         = {2522-5839},
        url          = {https://doi.org/10.1038/s42256-025-01019-5}
}

InstaNovo-P

If you use our InstaNovo-P model, finetuned on phosphorylated data, please cite our preprint: InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics:

@article {Lauridsen_2025_instanovo-p,
    author = {Lauridsen, Jesper and Ramasamy, Pathmanaban and Catzel, Rachel and Canbay, Vahap
        and Mabona, Amandla and Eloff, Kevin and Fullwood, Paul and Ferguson, Jennifer and
        Kirketerp-M{\o}ller, Annekatrine and Goldschmidt, Ida Sofie and Claeys, Tine and van
        Puyenbroeck, Sam and Lopez Carranza, Nicolas and Schoof, Erwin M. and Martens, Lennart and
        Van Goey, Jeroen and Francavilla, Chiara and Jenkins, Timothy Patrick and Kalogeropoulos,
        Konstantinos},
    title = {InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics},
    elocation-id = {2025.05.14.654049},
    year = {2025},
    doi = {10.1101/2025.05.14.654049},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2025/05/18/2025.05.14.654049},
    eprint = {https://www.biorxiv.org/content/early/2025/05/18/2025.05.14.654049.full.pdf},
    journal = {bioRxiv}
}

InstaNexus

If you use our generalizable, end-to-end workflow for direct protein sequencing, InstaNexus, please cite our preprint: Generalizable direct protein sequencing with InstaNexus:

@article {Reverenna_2025_instanexus,
    author = {Reverenna, Marco and Wennekers Nielsen, Maike and Wolff, Darian Stephan and Lytra,
        Elpida and Colaianni, Pasquale D. and Ljungars, Anne and Laustsen, Andreas H. and Schoof,
        Erwin M. and Van Goey, Jeroen and Jenkins, Timothy P. and Lukassen, Marie V. and Santos,
        Alberto and Kalogeropoulos, Konstantinos},
    title = {Generalizable direct protein sequencing with InstaNexus},
    elocation-id = {2025.07.25.666861},
    year = {2025},
    doi = {10.1101/2025.07.25.666861},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2025/07/31/2025.07.25.666861},
    eprint = {https://www.biorxiv.org/content/early/2025/07/31/2025.07.25.666861.full.pdf},
    journal = {bioRxiv}
}

Winnow

If you use our model-agnostic framework for estimating FDR from calibrated de novo sequencing output, Winnow, please cite our preprint: De novo peptide sequencing rescoring and FDR estimation with Winnow:

@article{mabona2025novopeptidesequencingrescoring,
        title={De novo peptide sequencing rescoring and FDR estimation with Winnow},
        author={Amandla Mabona and Jemma Daniel and Henrik Servais Janssen Knudsen and Rachel Catzel
        and Kevin Michael Eloff and Erwin M. Schoof and Nicolas Lopez Carranza and Timothy P. Jenkins
        and Jeroen Van Goey and Konstantinos Kalogeropoulos},
        year={2025},
        eprint={2509.24952},
        archivePrefix={arXiv},
        primaryClass={q-bio.QM},
        url={https://arxiv.org/abs/2509.24952},
}