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Many biological processes in plants are regulated through dynamic protein post-translational modifications (PTMs) such as phosphorylation and S-nitrosylation. Over the years, we have introduced several chemical proteomics strategies and tools for the characterization and measurement of PTMs in plants. For example, we introduced a proteomic strategy using isotope-labeled in vitro phosphorylation reactions and in vivo phosphorylated peptides as substrate pools and apply this strategy to identify putative substrates of nine protein kinases that function in plant abiotic and biotic stress responses (PNAS, 2020). We also quantitatively profiled global S-nitrosylation in wild-type Arabidopsis and mutants and identify over 2,000 S-nitrosylation peptides, including many previously unrevealed S-nitrosylated proteins (Nature Comm, 2023). These tools provide valuable resources for studies on dynamic plant regulation in plants, in particular in response to environmental stresses.