EasySCP unveils extensive liver zonation at single-cell proteomics resolution

The broader application of single-cell proteomics (SCP) in biology has been limited by complex workflows and reliance on specialized instrumentation. Here we present EasySCP, a high-throughput method that integrates FACS-based single-cell sorting, an all-in-one, single-step digestion process in 384-well plates, and sensitive mass spectrometry. EasySCP identifies nearly 5000 proteins from individual HEK293 cell. Applied to female murine liver, EasySCP achieves spatially informed proteomics profiling of hepatocytes zonation, detecting an average of 3500 proteins per hepatocyte and uncovering zonation patterns for 3277 out of 5267 proteins. Building on 215 conserved zonation markers, we further develop hepatocyte spatial status score (HSS) that enables reconstruct liver zonation across single-cell and multi-omics datasets. Together, our study introduces EasySCP, a broadly accessible tool for dissecting cellular heterogeneity at single-cell proteomics resolution in both healthy and disease states, effectively bridging the gap between transcriptomics and functional proteomics. Single-cell proteomics’ (SCP) application in biology is limited by complex workflows and reliance on specialized instrumentation. Here the authors present EasySCP, a high-throughput SCP method integrating FACS sorting, one-step digestion, and sensitive MS to achieve spatially informed proteomics.