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000280783 1001_ $$00009-0001-4570-1068$$aBurankova, Yuliya$$b0
000280783 245__ $$aPrivacy-preserving multicenter differential protein abundance analysis with FedProt.
000280783 260__ $$aLondon$$bNature Research$$c2025
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000280783 520__ $$aQuantitative 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.
000280783 536__ $$0G:(DE-HGF)POF4-352$$a352 - Disease Mechanisms (POF4-352)$$cPOF4-352$$fPOF IV$$x0
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000280783 650_2 $$2MeSH$$aHumans
000280783 650_2 $$2MeSH$$aProteomics: methods
000280783 650_2 $$2MeSH$$aMass Spectrometry
000280783 650_2 $$2MeSH$$aEscherichia coli: metabolism
000280783 650_2 $$2MeSH$$aPrivacy
000280783 650_2 $$2MeSH$$aAlgorithms
000280783 7001_ $$aAbele, Miriam$$b1
000280783 7001_ $$00000-0002-4169-9669$$aBakhtiari, Mohammad$$b2
000280783 7001_ $$00000-0002-4132-4322$$avon Toerne, Christine$$b3
000280783 7001_ $$aBarth, Teresa K$$b4
000280783 7001_ $$00000-0002-1165-7804$$aSchweizer, Lisa$$b5
000280783 7001_ $$0P:(DE-2719)9001718$$aGiesbertz, Pieter$$b6$$udzne
000280783 7001_ $$00000-0002-2026-9715$$aSchmidt, Johannes R$$b7
000280783 7001_ $$00000-0001-6121-7105$$aKalkhof, Stefan$$b8
000280783 7001_ $$00000-0001-6081-5664$$aMüller-Deile, Janina$$b9
000280783 7001_ $$00000-0002-7898-9408$$avan Veelen, Peter A$$b10
000280783 7001_ $$00000-0003-3265-3332$$aMohammed, Yassene$$b11
000280783 7001_ $$00000-0002-1507-0402$$aHammer, Elke$$b12
000280783 7001_ $$00000-0001-7990-8385$$aArend, Lis$$b13
000280783 7001_ $$00000-0002-9418-4386$$aAdamowicz, Klaudia$$b14
000280783 7001_ $$00000-0002-7922-7595$$aLaske, Tanja$$b15
000280783 7001_ $$aHartebrodt, Anne$$b16
000280783 7001_ $$aFrisch, Tobias$$b17
000280783 7001_ $$aMeng, Chen$$b18
000280783 7001_ $$aMatschinske, Julian$$b19
000280783 7001_ $$aSpäth, Julian$$b20
000280783 7001_ $$aRöttger, Richard$$b21
000280783 7001_ $$aSchwämmle, Veit$$b22
000280783 7001_ $$00000-0002-1630-6827$$aHauck, Stefanie M$$b23
000280783 7001_ $$0P:(DE-2719)2181459$$aLichtenthaler, Stefan F$$b24
000280783 7001_ $$00000-0003-2993-8249$$aImhof, Axel$$b25
000280783 7001_ $$00000-0003-1292-4799$$aMann, Matthias$$b26
000280783 7001_ $$00000-0002-6131-7322$$aLudwig, Christina$$b27
000280783 7001_ $$00000-0002-9094-1677$$aKuster, Bernhard$$b28
000280783 7001_ $$00000-0002-0282-0462$$aBaumbach, Jan$$b29
000280783 7001_ $$0P:(DE-2719)9002089$$aZolotareva, Olga$$b30$$udzne
000280783 773__ $$0PERI:(DE-600)3029424-1$$a10.1038/s43588-025-00832-7$$gVol. 5, no. 8, p. 675 - 688$$n8$$p675 - 688$$tNature computational science$$v5$$x2662-8457$$y2025
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