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Background   C. sinensis  is an important economic crop with fluoride over-accumulation in its leaves, which poses a serious threat to human health due to its leaf consumption as tea. Recently, our study has indicated that cell wall proteins (CWPs) probably play a vital role in fluoride accumulation/detoxification in  C. sinensis . However, there has been a lack in CWP identification and characterization up to now. This study is aimed to characterize cell wall proteome of  C. sinensis  leaves and to develop more CWPs related to stress response. A strategy of combined cell wall proteomics and N-glycoproteomics was employed to investigate CWPs. CWPs were extracted by sequential salt buffers, while N-glycoproteins were enriched by hydrophilic interaction chromatography method using  C. sinensis  leaves as a material .  Afterwards all the proteins were subjected to UPLC-MS/MS analysis.    Results  A total of 501 CWPs and 195 CWPs were identified respectively by cell wall proteomics and N-glycoproteomics profiling with 118 CWPs in common. Notably, N-glycoproteomics is a feasible method for CWP identification, and it can enhance CWP coverage. Among identified CWPs, proteins acting on cell wall polysaccharides constitute the largest functional class, most of which might be involved in cell wall structure remodeling. The second largest functional class mainly encompass various proteases related to CWP turnover and maturation. Oxidoreductases represent the third largest functional class, most of which (especially Class III peroxidases) participate in defense response. As expected, identified CWPs are mainly related to plant cell wall formation and defense response.    Conclusion  This was the first large-scale investigation of CWPs in  C. sinensis  through cell wall proteomics and N-glycoproteomics. Our results not only provide a database for further research on CWPs, but also an insight into cell wall formation and defense response in  C. sinensis .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03166-4.

Investigation of cell wall proteins of C. sinensis leaves by combining cell wall proteomics and N-glycoproteomics