GoBioSpace' depositors

GoBioSpace is a tool to turn measured masses into source tagged sum-formulas and with this blog entry I want to focus on the datasources.

new mass spectral library made available

Today I exported the current mass spectral library and linked the files on the GMD download web page.

severe bug in functional group prediction

Jan Lisec pointed me to a severe bug in the functional group prediction feature implemented in the GMD. It turned out that I normalised spectra before decision tree training different than spectra for spectral classification. Jan pointed me to a spectrum where the Phosphoric Acid Deriv group was predicted present based on m/z 299 although this particular mass had only a minimal intensity in this GC-MS spectrum.
The only good news is that the validation for the publication was not affected by this bug, because the cross validation is performed without this web interface. However, I removed this bug and want to apologise for this inconvenience.


Thanks Jan!

cheers,
the other Jan ;-)

GMD web site polished with JavaScript controls from HighCharts and ChemDoodle

I just finshed some work on the GMD website to improve the usability. I replaced images of mass spectra with interactive JavaScript controls from HighCahrts where the user can zoom in without any effort. An example mass spectrum of Alanine (3TMS) can be seen here. I also used this control to visualise the nort-south-plot in the mass spectral matching result view. It took me some time to figure all the settings out and still it is not perfect, bcause the data labels of the mass peaks are rendered accross the mass peak.
in the same breath I replaced all images of chemical structures by interactive JavaScript controls from ChemDoodle Web Components. The old images were rendered using the the Hyleos .Net ChemLib control which failed to rendere some of the more complex structures.

However, I appreciate this free resources from ChemDoodle and HighCharts very much!

cheers
Jan

GoBioSpace goes R

With the grateful help of Duncan Temple Lang (SSOAP package on omegahat, http://www.omegahat.org/SSOAP/ ) I could integrate GobioSpace with R.

GoBioSpace Features Isotope and Adduct Identification

I just released a new version 2.1.2.0 of the GoBioSpace search aplication which is now capable to connect single masses in retention time, accurate mass and intensities lists based on the ¹²C and ³⁴S isotopic patterns.

Transfering Retention Indexes

Gas chromatography (GC) coupled to mass spectroscopy (MS) relies on two cornerstones to identify metabolites in complex samples typically derived from plants. First, the retention index (RI, i.e. Kovats retention index), which is a number derived from the retention time and describes the chromatographic behaviour of the substances in a particular chromatographic setup. Second, the mass spectrum as shown here for Alanine (2TMS). We combine these features for convenience in to a mass spectral tag (MST) and link MSTs to the appropriate analytes.

Welcome

Hello,
I created this blog to provide updates and other usefull information around the Golm Metabolome Database.

greetings,
Jan