Table 8.
Metabolomic databases relevant to organelle analysis.
| Database | Focus | Features | Website | Reference |
|---|---|---|---|---|
| Library and Database of Toxic Compounds | Toxicological substances | Analysis done with LC-QTOF-MS, positive and negative ESI, high accuracy MS; contains over 7500 toxicology-relevant analytes; some standards spiked into either blood or/and urine matrix | NA | Broecker, 2011307 |
| Manchester Metabolomics Database | Serum, urine, yeast intracellular extracts, yeast, placental tissue; overlap with other databases | Accurate ESI-MS spectra, theoretical isotope abundance data, and ion types; 1,065 commercially available compound spectra performed with UPLC-MS and GC-MS; overlap with HMDB, KEGG, LIPID Maps, BioCyc, and DrugBank; provides a total of 42,687 compounds | www.dbkgroup.org/MMD/ | Brown 2009308 |
| KEGG Database | Encyclopedia of genes and genomics | Provide relevant information on cells, organisms, and organelles; connects gene catalogs to cell function, organism status, and ecosystem; is publically available | www.genome.jp/kegg/ | Kanehisa, 2011309 |
| FiehnLib GC-MS | Volatile metabolites below 550 Da | Contains GC-MS and some additional LC-MS/MS; it has some overlap with the BioMeta/KEGG database and the Golm Metabolite Database; supports BinBase | http://fiehnlab.ucdavis.edu/projects/FiehnLib/ | Kind, 2009310 |
| Golm Metabolite Database | Biological active metabolites | GC-MS detection, MS spectra and chromatograms | http://gmd.mpimp-golm.mpg.de/ | Kopka, 2004311 |
| KNApSAcK | Plant secondary metabolites | Chromatogram peak identification, over 49,000 specie-metabolite relations with over 24,000 metabolites; is publically available | http://kanaya.naist.jp/KNApSAcK/ | Oikawa, 2006312 |
| BinBase MS Database | Volatile compounds | GC-TOF-MS; contains over 1500 database entries for compounds from 18 species or 3435 samples; links to chemical and biochemical databases; web queries are possible | http://binbase.sourceforge.net | Skogerson, 2011313 |
| Yeast Metabolome Database | Yeast small molecules | Contains experimental intracellular and extracellular metabolites detected from both MS and NMR; contains more than 2000 metabolites collected from a literature review of yeast metabolites; mass spectrometry data from over 995 different genes/proteins. | http://www.ymdb.ca/ | Jewison, 2012314 |
| Plant Metabolome Database | Plant secondary metabolites of plants | Contains primary and secondary metabolites specific to plants; contains more than 1,000 metabolites with three-dimensional structures; chemical information overlap with KEGG and PubChem | http://www.sastra.edu/scbt/pmdb/ | Udayakumar, 2012315 |
| Chemical Entities of Biological Interest | Small chemical compounds, biological and synthetic | Merger of the IntEnz, Kegg, PDBeChem, and ChEMBL databases; contains mass, formulas, structures, and database links; publically available | http://www.ebi.ac.uk/chebi/ | Degtyarenko, 2008316 |
| Human Metabolome Database | Human metabolites, associated enzymes and transporters, and disease-related properties | Contains metabolites, enzyme responsible for production of metabolites; contains over 6800 entries and 3800 lipids, information pathway, abundance, and disease related properties as well as spectral databases, NMR, LC-MS, and GC-MS data | http://www.hmdb.ca/ | Wishart, 2009317 |
| National Institute of Standards and Technology | Identify species based on chemical formula | Contains compounds with most prominently electron ionization mass spectrometry data; properties such as thermodynamic data, IR spectrum, mass spectrum, UV/Vis spectrum, and vibrational and electronic energy levels | http://www.nis t.gov/pml/data/index.cfm | Wagner, 2003318 |
| METLINE | Endogenous metabolites | Freely accessible database containing high resolution Fourier transform mass spectrometry, tandem mass spectrometry, and LC/MS data | http://metlin.scripps.edu/ | Smith, 2005319 |
| MASSBANK | Analytes including endogenous metabolites | Contains mass spectral data for many types of compounds; contains primary and secondary metabolites | http://www.massbank.jp/?lang=en | Horai, 2010320 |
| Database of Bacterial Lipoproteins | Bacterial lipoproteins | Contains 278 lipoproteins and predicted lipoproteins from bacterial genomes; 773 different lipoproteins from the Swiss-Prot database were identified and grouped into 278 clusters containing protein orthologs; contains information for predicting the molecular function of the lipoprotein. | NA | Babu, 2006321 |
| LIPIDMaps | Biologically relevant lipids | Contains lipid-associated protein sequences, annotations, and genes associated with lipids; proteins are also classified to associate with the different LIPIDMaps; contains structures, studies from core laboratories, and simulations for appropriate lipids; structures can be searched based on name or structure. | http://www.lipidmaps.org/data/databases.html | Sud, 2007322 |
| DrugBank | Drug data and drug information | Contains over 4,100 drugs and 14,000 drug targets; contains drug properties and links to other databases such as PubMed and KEGG | http://www.drugbank.ca/ | Wishart, 2006323 |