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Burankova, Y.* ; Abele, M.* ; Bakhtiari, M.* ; von Toerne, C. ; Barth, T.K.* ; Schweizer, L.* ; Giesbertz, P.* ; Schmidt, J.R.* ; Kalkhof, S.* ; Müller-Deile, J.* ; van Veelen, P.A.* ; Mohammed, Y.* ; Hammer, E.* ; Arend, L.* ; Adamowicz, K.* ; Laske, T.* ; Hartebrodt, A.* ; Frisch, T.* ; Meng, C.* ; Matschinske, J.* ; Späth, J.* ; Röttger, R.* ; Schwämmle, V.* ; Hauck, S.M. ; Lichtenthaler, S.F.* ; Imhof, A.* ; Mann, M.* ; Ludwig, C.* ; Kuster, B.* ; Baumbach, J.* ; Zolotareva, O.*

Privacy-preserving multicenter differential protein abundance analysis with FedProt.

Nat. Comput. Sci., DOI: 10.1038/s43588-025-00832-7 (2025)
Verlagsversion Forschungsdaten DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises serious privacy concerns. Here we introduce FedProt, the first privacy-preserving tool for collaborative differential protein abundance analysis of distributed data, which utilizes federated learning and additive secret sharing. In the absence of a multicenter patient-derived dataset for evaluation, we created two: one at five centers from E. coli experiments and one at three centers from human serum. Evaluations using these datasets confirm that FedProt achieves accuracy equivalent to the DEqMS method applied to pooled data, with completely negligible absolute differences no greater than 4 × 10-12. By contrast, -log10P computed by the most accurate meta-analysis methods diverged from the centralized analysis results by up to 25-26.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Mass-spectrometry; Genes; Metaanalysis; Powerful; Package
ISSN (print) / ISBN 2662-8457
e-ISSN 2662-8457
Zeitschrift Nature Computational Science
Verlag Springer
Verlagsort Campus, 4 Crinan St, London, N1 9xw, England
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) CF Metabolomics & Proteomics (CF-MPC)
Förderungen Technische Universitat Munchen
Project SyMBoD
German Federal Ministry of Education and Research (BMBF)
European Union's Horizon Research and Innovation program
CVDLINK project
Lander
Funds of the Excellence Strategy of the Federal Government
Universitat Hamburg
Federal Ministry of Education and Research (BMBF)
Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
European Union's Horizon2020 research and innovation program