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[2]
method name M[2] (EIQTMS)
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 8000 or GC 8000 Top (ThermoQuest, Manchester, UK)
injection 1 µl splitless, 230C, 2 min
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 1 min at 70 C, 6 min ramp to 76 C, 45 min ramp to 350C, 1 min at 350 C, 10 min at 330C
carrier gas Helium, 1 ml min-1
mass spectrometer MD 800 MS, Voyager MS or Trace MS (ThermoQuest, Manchester, UK), transfer line 250C, ion source 200C
ionization electron impact
scanning 2 spectra s-1 (m/z = 40-600)
deconvolution AMDIS (Automated Mass Spectral Deconvolution and Identification System, National Institute of Standards and Technology, Gaithersburg, MD, USA)
settings adjacent peak subtraction (2), resolution (low), sensitivity (very low -medium), shape requirements (low)
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