PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals.

Cell Rep Methods

Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Biomedical Informatics & Data Science, Yale Univeristy School of Medicine, New Haven, CT 06510, USA. Electronic address:

Published: September 2024

To support PTM proteomic analysis and annotation in different species, we developed PTMoreR, a user-friendly tool that considers the surrounding amino acid sequences of PTM sites during BLAST, enabling a motif-centric analysis across species. By controlling sequence window similarity, PTMoreR can map phosphoproteomic results between any two species, perform site-level functional enrichment analysis, and generate kinase-substrate networks. We demonstrate that the majority of real P-sites in mice can be inferred from experimentally derived human P-sites with PTMoreR mapping. Furthermore, the compositions of 129 mammalian phosphoproteomes can also be predicted using PTMoreR. The method also identifies cross-species phosphorylation events that occur on proteins with an increased tendency to respond to the environmental factors. Moreover, the classic kinase motifs can be extracted across mammalian species, offering an evolutionary angle for refining current motifs. PTMoreR supports PTM proteomics in non-human species and facilitates quantitative phosphoproteomic analysis.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11440062PMC
http://dx.doi.org/10.1016/j.crmeth.2024.100859DOI Listing

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