PTMspesifiset

PTMspesifiset is a conceptual framework in proteomics designed to organize information about the substrate and site specificities of enzymes that catalyze post-translational modifications (PTMs). The term represents an effort to combine curated data on which residues are modified, by which enzymes, under what conditions, and within what sequence and structural context. It is intended as a basis for interoperable data resources rather than a single database.

Scope and data model: Each entry typically includes enzyme identity, the type of PTM (phosphorylation, acetylation, ubiquitination, glycosylation, methylation, among others), the target substrate, the modification site position, and the surrounding sequence motif or structural features that govern recognition. The model also records experimental evidence, species, cellular conditions, and any known cross-talk with other PTMs. Ontologies and controlled vocabularies are encouraged to ensure consistent annotation and enable cross-database queries.

Implementation and integration: PTMspesifiset is envisioned as a modular resource that can be populated from literature, high-throughput proteomics data, and computational predictions. It emphasizes provenance, with links to primary studies and data repositories, and interoperable formats for data exchange. Integration with existing resources such as protein databases and PTM-specific resources is considered essential to avoid duplication and to support richer queries.

Applications and challenges: The framework aims to support comparative analyses of PTM specificity across species, pathway modeling, and hypothesis generation for experiments and drug discovery. Challenges include data heterogeneity, inconsistent site annotation, evolving PTM definitions, and the need for community curation and governance to maintain data quality.