Table 3.
Overview of databases and resources for lipidomics grouped by classification, specific support for lipids, general availability of lipid structures, support for different levels of structural resolution (shorthand notation), main type of lipid ontology supported, availability of mass spectral data, availability and cross-linking of biochemical reaction data and curation model. Remarks: (1) kingdom, superclass, class, subclass. (2) internal and through MassIVE. (3) via integration with multiple tools. (4) via MassIVE and other public repositories. (5) via search. (6) local and linked via SPLASH [119] to MONA, MassBank. (7) via search and shorthand abbreviation. (8) Original and Liebisch 2020. (9) via Metabolomics Workbench. (10) GP and GL only. (11) based on the submission format (Mass Bank format). (12) via reference to spectral data. (13) based on submission format ISA-Table. (14) based on submission format mwTab. (15) others are available, e.g., LIPID MAPS, SwissLipids. (16) metabolic pathways of lipid mediators. (17) not necessarily machine readable.
| Category | Name | Main Purpose | Lipid Specific | Lipid Structures | Structural Levels | Ontology | Spectral Data | Biochemical Reaction Data |
Curation |
|---|---|---|---|---|---|---|---|---|---|
| Database | CCS-Compendium | Compendium of experimentally acquired Collisional Cross Section (Ion Mobility) data from molecular standards acquired on drift tube instruments | yes | yes | yes (1) | ClassyFire/ChemOnt | no | no | manual |
| Database | Panomics CCS | Collisional Cross Section (Ion Mobility) Database for Metabolites and Xenobiotics acquired on drift tube instruments | no | yes | no | no | no | yes | manual |
| Database | GNPS | Knowledge base for raw, processed or annotated fragmentation mass spectrometry data | no | yes | no | - | yes (2) | yes (3) | no (4) |
| Database | HMDB | Curated database of small molecule metabolites found in the human body | no | yes | yes (5) | ClassyFire/ChemOnt | yes (6) | yes | manual |
| Database | LIPID MAPS | Curated portal for LIPID MAPS lipid classification, experimentally determined structures, in-silico combinatorial structures and other lipid resources | yes | yes | yes (7) | LIPID MAPS (8) | yes (9) | yes | manual |
| Database | LipidHome | In-silico generated theoretical lipid structures | yes | yes (10) | no | Liebisch 2013 | no | no | manual |
| Database | SwissLipids | Curated database of lipid structures with experimental evidence and integration with biological knowledge and models | yes | yes | yes | Liebisch 2013 | no | yes | manual |
| Repository | MassBank | Curated database of mass spectrometry reference spectra | no | no | no | - | yes | no | manual (11) |
| Repository | MetaboLights | Repository for metabolomics data (MS and Nuclear Magnetic Resonance (NMR)) and metadata | no | yes | no | ChEBI | yes (12) | no | manual (13) |
| Repository | Metabolomics Workbench | Repository for metabolomics data (MS and NMR) and metadata | no | yes | yes | RefMet | yes | no | manual (14) |
| Repository | Metabolonote | Wiki-based repository for metabolomics metadata | no | no | no | - | yes (12) | no | manual |
| Repository | MetabolomeXchange | Aggregator of metabolomics metadata from MetaboLights, Metabolomics Workbench, Metabolonote and Metabolomic Repository Bordeaux | no | no | no | - | no | no | no |
| Repository | METASPACE | Repository for imaging mass spectrometry for metabolomics | no | yes | no | HMDB/ClassyFire/ChemOnt (15) | yes | no | manual |
| Resource | LimeMap | Curated CellDesigner XML and Vanted GML graph of lipid mediator pathways | yes | no | no (15) | - | no | yes (16) | manual |
| Resource | LipidWeb | Literature review and biochemistry of lipids | yes | yes (17) | no | - | yes (17) | yes (17) | manual |