P3DB-4.0: a large-scale plant protein phosphorylation database from diverse species to phosphosite conservation

Since the last version (version 3) of the P3DB was published in 2014, we are very encouraged to see that more and more plant scientists have been using our database including reanalysis of our data collections. In this new version (version 4.0), we extensively re-innovated our database to a brand-new platform (https://www.p3db.org) for accommodating much more data sets and new bioinformatic modules, many of which are suggested by our users and collaborators. In detail, we would like to highlight our novel development from the following aspects: (1) The new P3DB altogether harvests ~220,000 phosphosites in ~57,000 phosphoproteins curated across 45 plant species from ~260 in-vivo proteomic studies (compared with 48,000 phosphosites in 16,000 proteins from 9 species in version 3, almost 5 times more). We also integrated a large collection of protein-protein interaction data in these plant species. (2) With the rapid improvement of in-vitro Kinase Client (KiC) assay as well as increasing needs for kinase-specific phosphoproteomics, the new P3DB designs a scalable and informative network-based module in order to host and display these quantitative kinase substrate data. (3) With our large collection of the above data sets, we have invented a new module to search and visualize the divergence and convergence of the phosphorylation sites across orthologous peptides in many species. (4) Motivated by our collaborators, we have implemented a comprehensive PTM viewer to display multiple PTM sites, phosphorylation scores, and quantitative spectral counts all at one place. In summary, the new P3DB has been scaled up both in novel data sets, data types and tools, which enable our users to query and analyze comparative phosphoproteomics more conveniently and comprehensively. 

For Zoom information, please contact Robert Sanders (sandersrl@missouri.edu).