Computational protocol: Hepatic protection and anticancer activity of curcuma: A potential chemopreventive strategy against hepatocellular carcinoma

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Protocol publication

[…] The molecular composition of curcuma oil was analyzed on a two-dimensional gas chromatography time-of-flight mass spectrometer (GCxGC/TOF-MS). Stock solutions were then transferred to GC vials waiting for analysis. The methoxymation and derivatization were prepared immediately before the GCxGC/TOF-MS analysis.The Pegasus 4D GCxGC/TOF-MS instrument (LECO Corp., St. Joseph, MI, USA) was equipped with an Agilent 6890 gas chromatograph featuring a two-stage cryogenic modulator and secondary oven, 60 m × 0.25 mm i.d. × 0.25 μm film thicknesses, DB-5ms GC capillary column [(5%-phenyl)-dimethylpolysiloxane, Agilent Technologies J&W] was used as the primary column for the GCxGC/TOF-MS analysis. A second GC column of 1 m × 0.25 mm i.d. × 0.25 μm film thickness, DB-17ms [(50%-phenyl)-methylpolysiloxane, Agilent Technologies J&W] was placed inside the secondary GC oven after the thermal modulator.LECO’s ChromaTOF software package (version 4.21) equipped with the National Institute of Standards and Technology (NIST) MS database (NIST MS Search 2.0, NIST/EPA/NIH Mass Spectral Library; NIST 2008) was used for instrument control, spectrum deconvolution and metabolite identification. We used the manufacturer’s recommended parameters for ChromaTOF to reduce the raw instrument data into a metabolite peak list. These parameters are: baseline offset, 1; smoothing, Auto; peak width in first dimension, 15 sec; peak width in the second dimension, 0.1 sec; signal-to-noise ratio (S/N), 10; match required to combine peaks, 700; R.T. shift, 0.08 sec; minimum forward similarity match before name is assigned, 600. The peak true spectrum was also exported as part of the information for each peak in absolute format of intensity values. […]

Pipeline specifications

Software tools ChromaTOF, NIST MS Search
Application MS-based untargeted metabolomics
Organisms Mus musculus
Diseases Carcinoma, Hepatocellular, Chemical and Drug Induced Liver Injury