Exploring the feasibility of a single-protoplast proteomic analysis

Abstract

Background: Recent advances in high-resolution mass spectrometry have now enabled the study of proteomes at the single-cell level, offering the potential to unveil novel aspects of cellular processes. Remarkably, there has been no prior attempt to investigate single-plant cell proteomes. In this study, we aimed to explore the feasibility of conducting a proteomic analysis on individual protoplasts. Findings: As a result, our analysis identified 978 proteins from the 180 protoplasts, aligning with well-known biological processes in plant leaves, such as photosynthetic electron transport in photosystem II. Employing the SCP package in the SCoPE2 workflow revealed a notable batch effect and extensive missing values in the data. Following correction, we observed the heterogeneity in single-protoplast proteome expression. Comparing the results of single-protoplast proteomics with those of bulk leaf proteomics, we noted that only a small fraction of bulk data was detected in the single-protoplast proteomics data, highlighting a technical limitation of the current single-cell proteomics method. Conclusions: In summary, we demonstrated the feasibility of conducting a single-protoplast proteomic experiment, revealing heterogeneity in plant cellular proteome expression. This underscores the importance of analyzing a substantial number of plant cells to discern statistically significant changes in plant cell proteomes upon perturbation such as abscisic acid treatment in future studies. We anticipate that our study will contribute to advancing single-protoplast proteomics in the near future.