PTMoreR

PTMoreR enables cross-species PTM mapping and comparative phosphoproteomics through motif-centric analysis and BLAST-based data transfer for functional enrichment analysis between species.

Key Features:

• Motif-centric BLAST analysis: Considers surrounding amino acid sequences of PTM sites during BLAST to enable cross-species mapping.
• Sequence window similarity control: Controls sequence window similarity to map phosphoproteomic results between any two species.
• Site-level functional enrichment analysis: Performs functional enrichment analysis at the modification site level.
• Kinase-substrate network generation: Generates kinase-substrate networks from phosphoproteomic data.
• Cross-species phosphoproteome prediction: Predicts compositions of mammalian phosphoproteomes, demonstrated with 129 mammalian phosphoproteomes.
• Classic kinase motif extraction: Extracts classic kinase motifs across mammalian species for evolutionary refinement of motifs.

Scientific Applications:

• Cross-species phosphorylation site inference: Infers real P-sites in one species from experimentally derived P-sites in another species, demonstrated with mouse P-sites inferred from human P-sites.
• Environmental response protein identification: Identifies cross-species phosphorylation events on proteins with increased tendency to respond to environmental factors.
• Quantitative phosphoproteomic analysis: Facilitates quantitative phosphoproteomic analysis in non-human species.
• Evolutionary phosphoproteomics: Offers an evolutionary angle for refining current kinase motifs through cross-species comparison.

Methodology:

PTMoreR uses BLAST with consideration of surrounding amino acid sequences of PTM sites for motif-centric analysis, controlling sequence window similarity to map phosphoproteomic results between species.