Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity

Proteome remodeling is a fundamental adaptive response and proteins in complex and functionally related proteins are often co-expressed. Using a deep sampling strategy we define Arabidopsis thaliana tissue core proteomes at around 10,000 proteins per tissue and absolutely quantify (copy numbers per cell) nearly 16,000 proteins throughout the plant lifecycle. A proteome wide survey of global post translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. The deep proteome data is available from PRIDE submission PXD019330. Those results were complemented in this submission with parallel reaction monitoring (PRM) targeted proteomics over 1, 3 and 16 hours of flg22 exposure. The extensive coverage of the Arabidopsis proteome in various biological scenarios presents a rich resource to plant biologists that we make available to the community.