LIPID MAPS Proteome Database (LMPD)

Summary

LMPD organizes proteins and genes associated with lipid metabolism and connects them to lipid categories, enzyme reactions, Gene Ontology terms, and pathways. It complements the structure-centered LMSD by making the protein and gene components of lipid networks searchable [1,2].

Initial Construction

The first release identified human and mouse lipid-associated proteins through lipid-related Gene Ontology and KEGG annotations. It contained 2,959 protein records corresponding to about 2,300 unique genes, with roughly 1,600 human and 1,300 mouse proteins in the source list [1].

Each record assembled identifiers and annotations from resources including UniProt, Entrez Gene, ENZYME, GO, and KEGG. Search supported database identifiers, keywords, species, and lipid-class filters; record pages exposed gene names and locations, protein sequences and functions, EC numbers, pathways, related proteins, and splice variants [1].

Role in Integrated Analysis

LMPD was designed as the protein/gene side of lipid metabolic networks. Its mappings allow an analyst to move from a lipid class or biochemical reaction to candidate enzymes and genes, although the original keyword-based association procedure was acknowledged to require continued curation to control false positives and fill omissions [1].

The current LIPID MAPS infrastructure provides REST API access to LMPD alongside LMSD. BioPAN uses LMPD links to help users translate reaction-level lipid changes into species-specific candidate genes [2].

Citations

[1] Cotter et al. 2006. LMPD: LIPID MAPS proteome database. Supports: Initial record counts, protein-selection procedure, annotation sources, search fields, limitations, and network-integration objective. Location: Abstract; Bioinformatics; Query Forms; Record Details; Discussion.

[2] Conroy et al. 2024. LIPID MAPS: update to databases and tools for the lipidomics community. Supports: Current API availability and integration of LMPD with the broader platform. Location: Programmatic Access; Tools.