References

Citing ProteoPy

If you use ProteoPy in your research, please cite:

[FSGB26]

Fichtner ID, Sahm F, Gerstung M, and Bludau I. Proteopy: an anndata-based framework for integrated proteomics analysis. UNPUBLISHED, 2026.

@article{fichtner2026proteopy,
    title={ProteoPy: an AnnData-based framework for integrated proteomics analysis},
    author={Fichtner, Ian Dirk and Sahm, Felix and Gerstung, Moritz and Bludau, Isabell},
    journal={UNPUBLISHED},
    year={2026}
}

COPF algorithm

If you use the COPF proteoform inference functionality, please also cite:

[BFD+21]

Bludau I, Frank M, Dörig C, Cai Y, Heusel M, Rosenberger G, Picotti P, Collins BC, Röst H, and Aebersold R. Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nature Communications, 12:3810, 2021. URL: https://www.nature.com/articles/s41467-021-24030-x, doi:10.1038/s41467-021-24030-x.

@article{bludau2021systematic,
    title={Systematic detection of functional proteoform groups from bottom-up proteomic datasets},
    author={Bludau, Isabell and Frank, Max and D{\"o}rig, Christian and Cai, Yujia and Heusel, Moritz and Rosenberger, George and Picotti, Paola and Collins, Ben C. and R{\"o}st, Hannes and Aebersold, Ruedi},
    journal={Nature Communications},
    volume={12},
    pages={3810},
    year={2021},
    doi={10.1038/s41467-021-24030-x}
}