GOLM METABOLOME DATABASE

GoBioSpace

GoBioSpace (Golm Biochemical Space) is a repository of sum formula with source tagged annotations for properties such as InChI strings, CAS numbers, IUPAC names, synonyms, cross references or KEGG Pathway names, among others. The annotation source – the so called depositor – facilitates as a filter of biological relevance of sum formula. The meaningful interpretation of search results in a biological context is accomplished by a targeted search, limiting the formula to biology related depositors such as KEGG, BioCyc, Human Metabolome Database and Metabolome.JP, among others. In contrast, relaxed searches in regard to the formula’s depositor (i.e. including those sum formula only reported from vendors of potentially synthesised chemicals available in chemical focused databases PubChem Substance and ChemSpider) result in search hits with lower biological interpretability. To date, we collected more than 366 million meta information for 2.1 million unique sum formula from more than 150 public available databases (143 included in PubChem, downloaded May 2011). Our approach also enables the search against potentially putative sum formula such as depositor "Target Lipids" for Lipids.
For high resolution mass search queries, the accurate isotopic masses for either ambient 12C or fully isotopic labelled 13C, 15N, and 34S formula were calculated according to Böhlke et al (2005). Measured masses are mapped to sum formula, tolerating a given mass tolerance and considering user defined sets of expected analytical adducts and depositors to correct the measured masses and to filter for biological relevance, respectively. To make the mass search functionality accessible to the community, we integrated this as a web service into a graphical search application. The installation occurs via the ClickOnce technology (Microsoft) and requires Internet Explorer (Microsoft) or FireFox implemented with the Microsoft .NET Framework Assistant add-on. The .Net Framework 4.0 is also required. In case it is missing, a bootstrap installer will be provided automatically, but in this case, administrative privileges will be needed. In the client application, batches of masses to search can easily be configured (i.e. mass tolerance, adducts, depositors and restriction of sum formula hits based on atom number constraints) and the matching results are presented as browse-able and sort-able tables, which can be exported for further analysis into tabular formatted text files. However, the web services can be easily integrated into any data processing pipeline.
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We kindly ask users to cite Hummel J, Segu S, Li Y, Irgang S, Jueppner J and Giavalisco P (2011). Ultra performance liquid chromatography and high resolution mass spectrometry for the analysis of plant lipids. Front. Plant Sci. 2:54. doi: 10.3389/fpls.2011.00054 when publishing results derived from this service.

service last updated 17/02/2017 © 2008-2014 Golm Metabolome Database - All rights reserved
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