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

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机构: [1]Department of Pulmonary and Critical Care Medicine, Proteomics-Metabolomics Analysis Platform, and NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China [2]Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA [3]Information Research Institute, Tongji University, Shanghai 200092, China [4]State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240,China [5]Department of Medicine, Division of Nephrology, University of Connecticut School of Medicine, Farmington, CT 06030, USA [6]State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu 610041, China [7]Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA [8]Department of Biomedical Informatics & Data Science, Yale Univeristy School of Medicine, New Haven, CT 06510, USA
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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.Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.

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第一作者机构: [1]Department of Pulmonary and Critical Care Medicine, Proteomics-Metabolomics Analysis Platform, and NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China
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通讯机构: [1]Department of Pulmonary and Critical Care Medicine, Proteomics-Metabolomics Analysis Platform, and NHC Key Lab of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China [2]Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA [6]State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu 610041, China [7]Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA [8]Department of Biomedical Informatics & Data Science, Yale Univeristy School of Medicine, New Haven, CT 06510, USA
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