Single-cell proteomics has been applied to Arabidopsis root cells to differentiate between two closely related cell types, the cortex and endodermis. The study focused on isolated single cells from these regions, which originate from a common stem cell. Using single-cell proteomics, researchers identified 3,751 proteins and 1,114 proteins per cell from 756 cells. After stringent filtering, 3,101 proteins were quantified, with 555 proteins showing enriched expression in either the cortex or endodermis, allowing differentiation of these cell types. The study highlights the potential of single-cell proteomics to reveal cellular heterogeneity in plant cells. Challenges in applying single-cell proteomics to plants include the presence of cell walls and complex metabolites that complicate proteomic analysis. The study used fluorescence-activated cell sorting (FACS) to isolate single cells and developed a protocol for sample preparation and analysis. The results demonstrate the feasibility of single-cell proteomics in plants and its ability to distinguish between closely related cell types. The study also discusses the importance of considering cell size variability in plant single-cell proteomics and suggests future approaches to improve data quality and resolution. Overall, the findings underscore the promise of single-cell proteomics for exploring plant cellular heterogeneity and understanding biological processes at the single-cell level.Single-cell proteomics has been applied to Arabidopsis root cells to differentiate between two closely related cell types, the cortex and endodermis. The study focused on isolated single cells from these regions, which originate from a common stem cell. Using single-cell proteomics, researchers identified 3,751 proteins and 1,114 proteins per cell from 756 cells. After stringent filtering, 3,101 proteins were quantified, with 555 proteins showing enriched expression in either the cortex or endodermis, allowing differentiation of these cell types. The study highlights the potential of single-cell proteomics to reveal cellular heterogeneity in plant cells. Challenges in applying single-cell proteomics to plants include the presence of cell walls and complex metabolites that complicate proteomic analysis. The study used fluorescence-activated cell sorting (FACS) to isolate single cells and developed a protocol for sample preparation and analysis. The results demonstrate the feasibility of single-cell proteomics in plants and its ability to distinguish between closely related cell types. The study also discusses the importance of considering cell size variability in plant single-cell proteomics and suggests future approaches to improve data quality and resolution. Overall, the findings underscore the promise of single-cell proteomics for exploring plant cellular heterogeneity and understanding biological processes at the single-cell level.