MS2 Spectra Reference Databases
The MS2 databases are curated from multiple public repositories under various licenses as documented below.
By downloading these databases from the provided links below, you are considered to have agreed to comply with the original licenses.
Please read and ensure compliance with the requirements of these licenses if you decide to reuse any of these databases.
MS2 Fragmentation Formula Databases
The molecular formulas for the MS2 peaks in the reference database spectra are predicted using the MSBUDDY.
This fragmentation formula database was curated from the Complete library and Complete library (Neutral Loss) MS2 spectra databases above.
PLINK and hapmaps
These libraries are used for LD Clumping locally, including plink binary file and hapmaps curated from OpenGWAS.
Domain Enrichment Libraries
Microbial Metabolite, Exposure & Diet and Lipid Class Enrichment match compound names against a focused compound
database of their domain and test only the libraries of their domain. The databases and libraries were built on
2026-09-28 by tools/build_domain_libs.R of the MetaboAnalyst source code from the curated sources below; set and
compound counts of every library are listed in
domain_libraries.tsv.
A match to a library is an annotation by these sources, not evidence of microbial origin, intake or exposure in a study.
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Module
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Focused database
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Libraries and sources
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| Microbial Metabolite Enrichment |
Names are matched against a focused database of 5,645 compounds: 3,675 microbial metabolites (MiMeDB, Exposome-Explorer) and 1,970 compounds known only from KEGG gut bacterial pathways, which count only in the Gut bacterial pathways library. A name that is not found is not in these sources under that name. |
Microbial functions: 15 functional classes of gut microbial metabolites (short-chain fatty acids, bile acids, indoles, TMA / TMAO axis, ...); 899 compounds. Exposome-Explorer, MiMeDB
Microbial chemical classes: 113 chemical classes of microbial metabolites; 3,332 compounds. MiMeDB, Exposome-Explorer
Producing genera: 17 bacterial genera, each with the metabolites it produces; 157 compounds. Exposome-Explorer
Evidence of microbial origin: 3 sets: metabolites produced by human faecal bacteria, reduced by antibiotic treatment, reduced in germ-free animals; 451 compounds. Exposome-Explorer
Microbial transformations: 50 dietary or host substrates, each with its microbial transformation products; 158 compounds. Exposome-Explorer
Gut bacterial pathways: 123 KEGG metabolic pathways of common human gut bacteria; 2,706 compounds, 1,970 of them known only from these pathways, not as microbial metabolites. KEGG
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| Exposure & Diet Enrichment |
Names are matched against a focused database of 9,801 dietary and exposure compounds (FOBI, Exposome-Explorer, Phenol-Explorer, FooDB, dietary pattern studies, MarkerDB, SMPDB drug pathways, CDC NHANES, NORMAN-SLE PFAS lists). |
Food intake biomarkers: 153 foods and nutrients with the biomarkers that increase with their intake; 1,007 compounds. FOBI, Exposome-Explorer, Phenol-Explorer
Food intake biomarkers (all): 156 foods and nutrients (those above and 3 more) with the biomarkers that change with their intake in either direction; 1,019 compounds. FOBI, Exposome-Explorer, Phenol-Explorer
Dietary patterns: 12 dietary patterns (DASH, aMED, HEI-2015, EAT-Lancet, plant-based, Western, ultra-processed, ...) with the metabolites higher with adherence; 361 compounds. 7 studies (CRIC, ARIC, Framingham Offspring, WHI, AHS-2, FS2 and SHOPUS trials), linked to PubMed
Dietary patterns (all): 12 dietary patterns with the metabolites associated with adherence in either direction; 854 compounds. The same 7 studies
Food composition: 119 food groups with the compounds they contain; 4,248 compounds. FooDB, Phenol-Explorer
Food composition, by food: 334 single foods with the compounds they contain; 6,117 compounds. FooDB
Chemical exposures: 62 dietary and chemical exposures with their biomarkers; 238 compounds. MarkerDB
Environmental pollutants: 17 classes of environmental contaminants (PCBs, brominated and organophosphate flame retardants, phthalates and substitutes, PFAS, pesticides, ...) with their biomarkers measured in humans; 453 compounds. Exposome-Explorer, CDC NHANES, NORMAN-SLE PFAS lists
Drug pathways: 461 drug action and metabolism pathways; 884 compounds. SMPDB
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| Lipid Class Enrichment |
Lipid names are parsed (rgoslin, Shorthand 2020) and matched at their own level against a focused database of 190,104 entries (the MetaboAnalyst lipid database, LIPID MAPS and HMDB): 189,764 lipids in LIPID MAPS categories and main classes, and 340 compounds of the lipid pathways without a lipid category, which count only in the Lipid pathways library. A sum-composition name such as PC 34:1 matches the species PC 34:1, never one of its molecular species; a structure without an entry of its own is counted at its species. |
Lipid categories: 8 LIPID MAPS categories (glycerolipids, glycerophospholipids, sphingolipids, fatty acyls, sterol lipids, ...); 189,764 lipids, all lipids of the database with a category
Lipid classes: 48 LIPID MAPS main classes (glycerophosphocholines, ceramides, triradylglycerols, eicosanoids, ...), from LIPID MAPS or the head group of the name; 189,750 lipids
Lipid pathways: 288 lipid pathways (37 KEGG; 113 WikiPathways, 107 Reactome and 31 PathBank via RaMP-DB) restricted to the lipid database, a molecular species also counting for its sum composition; 1,410 compounds; 3 to 500 members. Reactome pathways that group sub-pathways of the library, overviews, drug action and mostly non-lipid pathways are left out
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