AI and the World's Hard Problems · Life sciences · Nature (machine learning) · 2026-10-05
ProFormer: generalizable classification of single-cell and plasma proteomes using deep learning
Current proteomic workflows have low throughput and require extensive data processing, which slows sample classification. ProFormer is a transformer-based deep-learning pipeline that takes MS1-level peptide ion features directly from mass spectrometry data. It outperformed traditional machine learning and CNNs across 14 architectures and classified single-cell proteomes by cell type, cycle stage, and differentiation trajectory, as well as patient disease status from plasma proteomes.