Dataset Card: Astral dataset PXD055983 for InstaNovo-P

Summary

This dataset was used to asses the ability of InstaNovo-P to generalize to unseen detector types.

To this end, we reprocessed the PXD055983 dataset acquired on an Orbitrap Astral instrument using the Astral detector with the same database search workflow as described in the InstaNovo-P paper.

Original data source:

Field	Value
Title	Differential protein expression in new1 knock-out yeast
Description	A label-free quantitative proteomics experiment was performed to study the impact of new1 knock-out on differential protein expression in S. cerevisiae (baker’s yeast).
HostingRepository	PRIDE
AnnounceDate	2026-02-04
AnnouncementXML	Submission_2026-02-04_01:43:28.657.xml
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jia-Xuan Chen
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Astral
URL	http://central.proteomexchange.org/cgi/GetDataset?ID=PXD055983

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        = { PXD055983 (Revision 953a031) },
    year         = 2026,
    url          = { https://huggingface.co/datasets/InstaDeepAI/PXD055983 },
    doi          = { 10.57967/hf/7816 },
    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}
}