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Edu-talk

이매스교육 및 공지사항

Edu-talk

  • 제목

    Mass / NMR Spectral Databases
  • 작성자

    이매스
  • 첨부파일

·         HMDB
The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body.  It contains experimental MS/MS data for 800 compounds, experimental 1H and 13C NMR data (and assignments) for 790 compounds and GC/MS spectral and retention index data for 260 compounds.  Additionally, predicted 1H and 13C NMR spectra have been generated for 3100 compounds.  All spectral databases are downloadable and searchable.
 
·         BMRB
The BioMagResBank (BMRB) is the central repository for experimental NMR spectral data, primarily for macromolecules.  The BMRB also contains a recently established subsection for metabolite data.  The current metabolomics database contains structures, structure viewing applets, nomenclature data, extensive 1D and 2D spectral peak lists (from 1D, TOCSY, DEPT, HSQC experiments), raw spectra and FIDs for nearly 500 molecules.  The data is both searchable and downloadable.
 
·         MMCD
The Madison Metabolomics Consortium Database (MMCD) is a database on small molecules of biological interest gathered from electronic databases and the scientific literature. It contains approximately 10,000 metabolite entries and experimental spectral data on about 500 compounds.  Each metabolite entry in the MMCD is supported by information in an average of 50 separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, information on the presence of the metabolite in different biological species, and extensive links to images, references, and other public databases.
 
·         MassBank
MassBank is a mass spectral database of experimentally acquired high resolution MS spectra of metabolites.  Maintained and supported by he JST-BIRD project, it offers various query methods for standard spectra obtained from Keio University, RIKEN PSC, and other Japanese research institutions.  It is officially sanctioned bythe Mass Spectrometry Society of Japan.  The database has very detailed MS data and excellent spectral/structure searching utilities.  More than 13,000 spectra from 1900 different compounds are available.
 
·         Golm Metabolome Database
The Golm Metabolome Database provides public access to custom GC/MS libraries which are stored as Mass Spectral (MS) and Retention Time Index (RI) Libraries (MSRI). These libraries of mass spectral and retention time indices can be used with the NIST/AMDIS software to identify metabolites according their spectral tags and RI's.  The libraries are both searchable and downloadable and have been carefully collected under defined conditions on several types of GC/MS instruments (quadrupole and TOF).
 
·         Metlin
The METLIN Metabolite Database is a repository for mass spectral metabolite data. All metabolites are neutral or free acids. It is a collaborative effort between the Siuzdak and Abagyan groups and Center for Mass Spectrometry at The Scripps Research Institute.  METLIN is searchable by compound name, mass, formula or structure.  It contains 15,000 structures, including more than 8000 di and tripeptides.  METLIN contains MS/MS, LC/MS and FTMS data that can be searched by peak lists, mass range, biological source or disease.
 
·         Fiehn GC-MS Database
This library contains data on 713 compounds (name, structure, CAS ID, other links) for which GC/MS data (spectra and retention indices) have been collected by the Fiehn laboratory.  A locally maintain program called BinBase/Bellerophon filters input GC/MS spectra and uses the spectral library to identify compounds.  The actual GC/MS library is available from several different GC/MS vendors.
 
·         BML-NMR
The Birmingham Metabolite Library Nuclear Magnetic Resonance database is a freely available resource containing 3328 NMR spectra of 208 common metabolite standards. This database includes both 2-D 1H J-resolved spectra and 1-D 1H spectra, recorded at 500 MHz using various water suppression methods and acquisition parameters, for solutions at pH values of 6.6, 7.0 and 7.4. The raw and processed data, including associated metadata, are housed in a purpose-built MySQL database that is compliant with the Metabolomics Standards Initiative (MSI) endorsed reporting requirements, with some necessary amendments. Library data can be accessed freely and searched through a custom written web interface. FIDs, NMR spectra and associated metadata can be downloaded according to a newly implemented MSI-compatible XML schema.
 
·         MetaboLights database
MetaboLights is a database for metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and experimental data from metabolic experiments. MetaboLights offer user-submission tools and have strong reporting capabilities. We will utilise and further develop de-facto standard formats where various components are encapsulated, such as the encoded spectral and chromatographic data, and associated information about the chemical structure, as well as metadata describing assays and the study as a whole.
 
·         mzCloud
mzCloud features a searchable collection of high resolution/accurate mass spectral trees using a new third generation spectra correlation algorithm. mzCloud is free and available for public use online. mzCloud also represents an open consortium of dedicated research and scientific groups aiming to establish a comprehensive library of high quality spectral trees to improve the structure elucidation of unknowns. mzCloud tries to address identification bottleneck by considering all mass spectrometricaly relevant aspects, looking at number of experimental and computational details and in some cases allowing identification of unknowns even if they are not present in library.