Dataset Card: 21PTM dataset PXD009449 for InstaNovo-P

To assess the model performance of InstaNovo-P on phosphorylated peptides, we used a subset of project PXD009449 as evaluation dataset.

Original data source:

Field	Value
Title	Systematic characterization of 21 post-translational modification using synthetic peptides
Description	The data presented in this study in the - context of the ProteoemTools project - is based on the synthesis of about 5000 synthetic
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:44:20.696.xml
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniel Zolg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; 3'-nitro-L-tyrosine; N6-malonyl-L-lysine; biotinylated residue; phosphorylated residue; acetylated residue;
Instrument	Orbitrap Fusion Lumos
URL	https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009449

Citation:

If you use InstaNovo-P in your research, please cite: InstaNovo-P: a de novo peptide sequencing model for phosphoproteomics

@article{lauridsen_kalogeropoulos_2026_instanovo-p,
    title = {InstaNovo-P: a de novo peptide sequencing model for phosphoproteomics},
    author = {Lauridsen, Jesper and Canbay, Vahap and Catzel, Rachel and Ramasamy, Pathmanaban 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},
    year = {2026},
    journal = {Nature Communications},
    volume = {17},
    number = {1},
    pages = {9277},
    doi = {10.1038/s41467-026-75138-x},
    publisher = {Springer Nature},
    url = {https://doi.org/10.1038/s41467-026-75138-x}
}

If you use this dataset, please cite

@misc{instadeep_ltd_2026,
    author       = { InstaDeep Ltd },
    title        = { PXD009449 (Revision 7676f2c) },
    year         = 2026,
    url          = { https://huggingface.co/datasets/InstaDeepAI/PXD009449 },
    doi          = { 10.57967/hf/7818 },
    publisher    = { Hugging Face }
}

If you use the InstaNovo model to generate predictions, please also cite: 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}
}