Provides data pertaining to biologically relevant small molecules from a variety of species. MMCD is a resource that contains information on more than 20,000 metabolites and other small molecules of biological interest chosen from entries in such databases as KEGG, BioCyc, CHEBI, HMDB, UM-BBD and PDB. The database is compatible with both nuclear magnetic resonance (NMR) and mass spectrometry (MS) data (singly or in combination) and facilitates high-throughput metabolomics investigations.
Provides access to metabolite information and tandem mass spectrometry data. METLIN is a metabolite database for metabolomics containing over 64,000 structures. It also contains a data management system designed to assist in metabolite researching by providing public access to its repository of current and comprehensive MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available on the METLIN website.
Combines quantitative chemical, physical, clinical and biological data about thousands of endogenous human metabolites. HMDB is a multi-purpose database with a strong focus on quantitative, analytic or molecular-scale information about metabolites, their associated enzymes or transporters and their disease-related properties. This online resource is designed to contain or link three kinds of data: (i) chemical data, (ii) clinical data and (iii) molecular biology/biochemistry data.
Stores raw experimental and associated metadata from metabolomics studies. MetaboLights is a general purpose, cross-species and cross-application database in metabolomics. Studies are created by researchers in ISA-Tab format, by either automatically creating datasets from in-house laboratory information management systems, or by manually creating ISA-Tab archives with the help of the ISA-tools suite. The species coverage of studies follows the preferences for model species around the globe.
An expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. ECMDB currently contains 3755 small molecules with 1402 associated enzymes and 387 associated transporters. It also has 1542 metabolic pathways that are linked to 3011 metabolites. A total of 19,294 NMR and MS spectra (experimental and predicted) for 3098 different E. coli metabolites are also contained in the database. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.
Contains metabolome and proteome data in plasma obtained from 5,093 healthy volunteers in a Japanese population. jMorp delivers minimized biases due the utilization of a single protocol in a single institute, the Tohoku Medical Megabank Cohort Study. It offers a graphical viewer that allows to display correlations between metabolites. This database is built using large-scale cohort data for healthy volunteers with various health records and genome data, and provides significant genome wide association study (GWAS) results.
A public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. The Metabolomics Workbench provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies.
Contains extensive metabolomic data and metabolic pathway diagrams about Pseudomonas aeruginosa. PAMDB integrates metabolites, their corresponding reactions, proteins involved and the complete metabolic pathways in a single database. This catalogue is constructed similarly to the long-established metabolome database series. This online resource is organized by categories: metabolites, proteins, reactions and pathways.
Facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS). The GMD comprises mass spectra and retention time indices of pure reference substances and frequently observed mass spectral tags (MST: mass spectrum linked to chromatographic retention) of yet unidentified metabolites.
An open-access metabolome database for tomato fruit. The database was developed with LC-MS data and primarily contains semipolar metabolites. MoTo DB also contains metabolite information from the literature and includes a variety of tomato fruit extracts from cultivated, wild, and transgenic tomato varieties. To search the database for a compound of interest, the mass is entered, either as a range or an accurate value, along with the ionization mode. The mass accuracy can also be set to accommodate data from a variety of detectors (low or high accuracy). The results pane displays the projected formula, a link to any PubChem identifiers, and CAS number as well as a link to the retention time, calculated accurate mass, MS/MS fragments, UV/visible spectral information, and alternative names for the compound (if any) and literature references.
Compiles metabolite annotations. KomicMarket is a database of annotations of metabolite peaks that were detected by mass spectrometers (MSs) in metabolomics studies. Data were obtained with high-resolution MSs connected to liquid chromatography. Based on comprehensive characterization of tomato fruit metabolites, this resource identifies chemical building blocks that appear frequently in the tomato fruit tissues.
Simplifies the recognition of metabolites incorporating isotopic labels. isoMETLIN is searchable thanks to 13C, 15N, 2H, and 18O isotopologues based on accurate mass and also includes experimental tandem mass spectrometry (MS/MS) data for several hundred isotopically labeled metabolites that will ease the identification of isotopomers. It can assist extending flux modeling to liquid chromatography coupled mass spectrometry LC/MS analyses.
Allows to inform about nontargeted metabolic profiling analysis using liquid chromatography-mass spectrometry (LC-MS). MS2T provides users structural information for the detected peaks in the metabolic profile data. It uses optimized methods for acquisition of a large amount of tandem mass spectrometry (MS/MS) data, and enables high-throughput acquisition of metabolic profiling data. The library can be applied for analysis of metabolic profile data acquired by using other liquid chromatography-mass spectrometry (LC-MS) methods that employ identical or compatible liquid chromatography (LC) conditions.
Allows to search and analyze ranging from metabolomics to transcriptomics. Provides users an access to data resources of PRIMe. The PRIMeLink web interface integrates three databases: the MS2T library, AtMetExpress and ReSpect. These several resources supply many information like un-targeted tandem mass spectrometry (MS/MS) data of plant metabolites, transcriptomics and metabolomics approaches in Arabidopsis developmental stages, or MS/MS data resources.
Provides high quality structures for reliable structure-based drug design (SBDD). KNApSAcK-3D offers 3D structures for all 50,048 metabolites, the relationships between metabolites and their expressing organism(s), contained in the original KNApSAcK database. It can be useful to discover new therapeutic applications for natural products. This database is manually curated and 3D structures are manually constructed.
A collection of literature and in-house MSn spectra data for research on plant metabolomics. As a main web application of ReSpect, a fragment search was established based on only the m/z values of query data and records. The confidence levels of the annotations were managed using the MS/MS fragmentation association rule, which is an algorithm for discovering common fragmentations in MS/MS data.
Gathers network pharmacology related interactions information at the systemic level. PhID aims to provides a repository for visualizing relationships between entities such as drugs, targets, diseases, genes, pathways, and side-effects. The database includes more than 306000 activities. Searches can be made by names, ids, molecular structures, or molecular fragments for different purposes.
Contains a complete list of all possible metabolites that have been detected in human urine using current technologies. The UMDB provides a list of the metabolite names, level of verification, normal and disease-associated concentration ranges, associated diseases and corresponding literature references for all human urine metabolites that have ever been detected and/or quantified in the literature. The UMDB also contains concentration data compiled from the experimental studies described here.
Provides the research community with comprehensive liver-related data, as well as to allow the community to share their liver-related data flexibly and efficiently. LiverWiki integrates liver-related genes, homolog genes, gene expressions in microarray datasets and RNA-Seq datasets, proteins, protein interactions, post-translational modifications, associated pathways, diseases, metabolites identified in the metabolomics datasets, and literatures for community-driven sharing.
An automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures. The vocBinBase DB is an extension of the previously reported metabolite BinBase software developed to track and identify derivatized metabolites. The BinBase algorithm uses deconvoluted spectra and peak metadata (retention index, unique ion, spectral similarity, peak signal-to-noise ratio, and peak purity) from the Leco ChromaTOF software, and annotates peaks using a multi-tiered filtering system with stringent thresholds. The vocBinBase algorithm assigns the identity of compounds existing in the database.
A semantic MediaWiki-based database designed specifically for managing metabolomic metadata. Metabolonote was developed with the aim to promote the publication and utilization of Metabolomics data by simplifying the metadata record process. The metadata in Metabolonote is referred from the record pages in Bio-MassBank by a URL link, which complements the detailed description of metadata in Bio-MassBank.
Collects data about metabolites implicated in resistance to Fusarium head blight(FHB). MWFD assists users in antifungal compound discovery and the development of resistant wheat varieties. It is a manually curated repository including information about compound properties and their reported inhibitory activities against known targets. Searches can be made by eight different queries such as compound name or MesH Term.
Permits to centralize multiple renowned metabolite databases. DIMEdb provides a web-based resource that contains more than 80,000 metabolites sourced from a number of renowned metabolite databases which can be utilized in the analysis and annotation of direct infusion mass spectrometery (DIMS) data. It also includes an application programming interface (API) which enables users to extract information from the integrated metabolite database.
Gathers information related with mass spectrometry. NIST Tandem Mass Spectral Library is a repository which consists of four mass spectral libraries coupled to a library of retention index (RI)/GC Method. The database provides data about 13 000 compounds, 570 000 tandem spectra as well as more than 118 000 precursor ions and supplies functionalities to index old libraries or to perform advanced searches by HiRes MS/MS or by InChIKeys.
A mass spectral tag archive for metabolomics. The MassBase database is fundamental for metabolomics, which provides raw mass chromatograms from various biological samples and text-file data processed from the raw chromatograms. You can view the raw or processed chromatograms of your interest and also download the files of interest or even in bulk all datasets.
Provides a collection of omics data dealing with small biomolecules. MDL aims to simplify the accessibility to nuclear magnetic resonance (NMR) parameters of small metabolites in liquid phase. It contains metabolites defining the primary cellular metabolism in the biosphere. This database offers several features, allowing users to plot symbolic spectra of a selected metabolite or to confront their own experimental data with those in the database.
Hosts a library of metabolic engineering strain designs and furnishes a standard for metabolic engineers. LASER compiles about 300 papers from scientific literature and more than 400 designs aiming to encompass the majority of genetically defined yeast and E. coli designs. The application can be used for design storing and analyzing and intends to ease the development of novel engineering tools.
A public repository of LC- and GC-MS data that analyzed biological cells and tissues. Most of the data are "Unknowns" or of tentative chemical structure. On the other, MassBank is a public repository of mass spectra that analyzed a "single" chemical compound with the "chemically defined" structure.
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