NanoPots is a nanoliter-scale sample preparation system that enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. NanoPOTS has been used for spatially resolved proteome measurements from clinical tissues from type 1 diabetics and control donors.