Privacy-Preserving Multi-Center Differential Protein Abundance Analysis with FedProt
This addresses privacy issues for researchers and institutions collaborating on proteomics data, though it is incremental as it applies existing federated learning techniques to a new domain.
The paper tackles the problem of privacy concerns in multi-center differential protein abundance analysis by introducing FedProt, a tool that uses federated learning and additive secret sharing to achieve accuracy equivalent to pooled data analysis with negligible differences (e.g., absolute differences ≤ 4×10^-12).
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 significant 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 LFQ E.coli experiments and one at three centers from TMT human serum. Evaluations using these datasets confirm that FedProt achieves accuracy equivalent to DEqMS applied to pooled data, with completely negligible absolute differences no greater than $\text{$4 \times 10^{-12}$}$. In contrast, -log10(p-values) computed by the most accurate meta-analysis methods diverged from the centralized analysis results by up to 25-27. FedProt is available as a web tool with detailed documentation as a FeatureCloud App.