The Comprehensive Systems Biology Project (CSB)
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- The Golm Metabolome Database -
msri
Hosted at Max Planck Institute of Molecular Plant Physiology
Databases: Associated DB | Transcriptome DB | Metabolome DB | Co-Response DB | BestFit
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NOTIFICATION: GMD has been migrated and will permanently be maintained on private servers.
Herewith we inform you that all CSB.DB databases have been migrated and associated services will be maintained on private servers since the beginning of 2016. This includes all gene correlation and expression databases (search the WWW for alternatives), the GMD@CSB.DB module (alternative will be reachable via http://gmd.mpimp-golm.mpg.de/) and all associated databases (terminated).
The BestFit software, a tool for non-aqueous fractionation data analysis, will be available by the Experimental Systems Biology Research Group headed by Dr. Patrick Giavalisco.
MS Method Information
 

Mass Spectra Information for Method: m[1]
method name M[1] (EITTMS)
sampling shock freezing in liquid nitrogen
extraction hot (70C) methanol/water/chloroform (approx. 4:1:2; v/v/v)
fractionation polar metabolites
liquid partitioning into methanol/water (approx. 1:1; v/v), and chloroform (chloroform phase is discarded)
derivatization =N-O-CH3 (methoxyamine hydrochloride/ pyridine reagent, 20 mg / ml) - Si(CH3)3 (N-methyl-N-(trimethylsilyl)-trifluoroacetamide, MSTFA reagent)
ri system n-dodecane (RI 1200)
n-pentadecane (RI 1500)
n-nonadecane (RI 1900)
n-docosane (RI 2200)
n-octacosane (RI 2800)
n-dotriacontane (RI 3200)
n-hexatriacontane (RI 3600)
gas chromatograph GC 6890 (Agilent Technologies, Palo Alto, CA, USA)
injection 1 µl splitless, 230C, 2 min pulse at 110 psi
column Rtx-5Sil MS, 30 m x 0.25 mm ID with 10 m integrated guard column, 0.25 µm film thickness (Restek GmbH, Bad Homburg, Germany)
temperature program 2 min at 80 C, 15 min ramp to 350 C, 2 min at 350 C
carrier gas Helium, 1 ml min-1, operated by electronic pressure control
mass spectrometer Pegasus II TOF-MS system (Leco, St. Joseph, MI, USA), transfer line 250C, ion source 200C
ionization electron impact
scanning 6 spectra s-1 (m/z = 70-600)
deconvolution AMDIS (Automated Mass Spectral Deconvolution and Identification System, National Institute of Standards and Technology, Gaithersburg, MD, USA)
settings adjacent peak subtraction (2), resolution (medium), sensitivity (high), shape requirements (high)
remarks Pure reference substances are processed without extraction and fractionation
method variants -Omission of fractionation for the analysis of a mixed polar and lipophilic fraction
-Omission of methoxyamination