METLIN Database

METLIN Metabolite Database (http //metlin.scripps.edu), a repository for mass spectral metabolite data. Each metabolite has a link to the Kyoto Encyclopedia of Genes and Genomes. 

The identification of the lipids is a very challenging task. The lack of comprehensive mass spectral libraries often limits the identification of compounds in LC-MS and shotgun methods. Some spectral libraries are available, such as the Human Metabolome Database (http /www.hmdb.ca), the METLIN Metabolite Database (http /metlin.scripps.edu) (24), and the MassBank (http /www. massbank.jp) (25). However, construction of universal spectral databases for API-MS is challenging due to the poor reproducibility and high interinstru-ment variability of fragmentation patterns. 

Finally, we will identify the structure of enriched ions by using accurate mass (obtained during our standard MS experiments) and searching metabolite databases, such as METLIN [75], PubChem [76], or the lipid MAPS [77] for... 

To use metabolic footprinting as a technique for high-throughput applications, benchmark spectra databases with identified peaks are required so that peak patterns obtained from MS or NMR analysis can be rapidly translated into relevant biological information. Common experimental procedures should, ideally, also be established for metabolite analysis [80] such as those existing in proteomics or transcriptomics. Nevertheless, the scientific community has only recently attempted to achieve these tasks. Several databases for identification of metabolomics signals by MS are now available, for instance, BIGG [81], BioCyc [82], MSlib [83], NIST [84], Metlin [85], and HMDB [86] databases. For a more comprehensive list of resources we refer to the review of Werner and coworkers [68]. 

Metlin Database. Available at www.metlin.scripps.edu. Accessed 20 Jan 2009... 

Smith CA, O Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G (2005) METLIN a metabolite mass spectral database. Ther Drug Monit 27(6) 747-751... 

Smith, C.A. et al., METLIN A metabolite mass spectral database, Then Drug Monit., 27(6), 747, 2005. 

With the advent of accurate mass instruments, access to a reference database or library of compounds with the exact masses of precursor and product ions is becoming increasingly important. Many instrument manufacturers, as well as independent companies or institutions, are developing software that allows chemists to manage this type of information for specific applications such as proteomics or chemical contaminants. Examples of online resources that may be useful for searching for unknown residues based on molecular formulas obtained from accurate mass data inciude Metlin from the Scripps Center for Mass Spectrometry and ChemSpider from the Royal Society of Chemistry. " ... 

C. Smith, G. O Maille, E. Want, C. Qin, S. A. Trauger, T. Brandon, D. Custodio, R. Abagyan, and G. Siuzdak. METLIN a metabolite mass spectral database. Therapeutic Drug Monitoring, 27 747-751, 2005. 

METLIN [10, 11] is a metabolomics database, which is a repository of metabolite information as well as tandem MS data. The METLIN database was developed and is maintained by Dr Siuzdak laboratory at The Scripps Research Institute. The METLIN metabolite database is available to the public online (http //metlin.scripps.edu) for metabolite searches. 

The METLIN metabolite database is implemented using the open-source software tool, MySQL. Most compounds are annotated with both a chemical formula and structure. Individual metabolite is linked to outside resources such as the KEGG, Human Metabolome Database (HMDB), and the respective PubChem database entries through the included numbers of KEGG, HMDB, and Chemical Abstract Service (CAS), respectively. This kind of linkage makes it easy for the researchers to find further references and inquiries about the metabolite. 

Overall, the METLIN database allows researchers to readily search and characterize metabolites through their chemical and/or physical features such as accurate mass, and single and multiple fragments including neutral-loss fragments. These capabilities of the database greatly facilitate the value of their metabolomics MS and MS/MS data and expedite the identification process. METLIN is one of the most used databases in metabolomics including lipidomics. 

Fig. 4.5 Identification workflow of ephedrine (a) peak was detected in electrospray positive ion mode (+ESI) extracting the m/z signal of ephedrine (b) MS spectrum was compared to database (c) database match with 4-hydroxymetamphetamine and ephedrine that actually having the same emparical formula. Once candidates were detected, sample was re-injected and MS/MS spectra acquired at several collision energies (d) MS/MS spectrum acquired were compared with (e) METLIN library MS/MS and the ephedrine was confirmed (Gonzdlez-Marino et al. 2012, Fig. 4.3, with permission)...

TheMetlin metabolics database (https //metlin.scripps.edu/index.php) ... 

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