CPLM 4.0: an updated database with rich annotations for protein lysine modifications

Area of Science:

• Biochemistry
• Proteomics
• Bioinformatics

Background:

• Protein lysine modifications (PLMs) are crucial post-translational modifications (PTMs) affecting protein function.
• Existing databases for PLMs lack comprehensive and up-to-date information.

Purpose of the Study:

• To report the compendium of protein lysine modifications (CPLM 4.0), an expanded and annotated data resource.
• To provide a comprehensive collection of experimentally identified PLM events for research.

Main Methods:

• Collected 450,378 PLM events from literature and public databases, integrating with PLMD 3.0 data.
• Annotated the data with 13 diverse biological and chemical aspects from 102 resources.
• Compiled a total of 592,606 PLM events across 29 types of PLMs in 219 species.

Main Results:

• CPLM 4.0 contains 592,606 modification events on 463,156 unique lysine residues in 105,673 proteins.
• The dataset is significantly larger (>2-fold increase) than previous versions and related resources.
• Comprehensive annotations cover variations, diseases, interactions, pathways, and more.

Conclusions:

• CPLM 4.0 represents a substantial advancement in PLM data resources.
• The database is poised to facilitate deeper investigations into the roles and functions of PLMs.
• This resource will be valuable for researchers in proteomics, molecular biology, and disease studies.