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.
Please follow the Golm Metabolome Blog to read more on updates and service
interruptions on account of maintenancs work.
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.
