Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15 000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry.

 

We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues.

 

Notably, profiling of N⁶-methyladenosine (m⁶A) across the rice major tissues shows that m⁶A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m⁶A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome.