Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA090871

Local Sample ID:	3WK_placebo_11_020
Subject ID:	SU001315
Subject Type:	Mammal
Subject Species:	Canis lupus familiaris
Taxonomy ID:	9615

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Subject:

Subject ID:	SU001315
Subject Type:	Mammal
Subject Species:	Canis lupus familiaris
Taxonomy ID:	9615

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
3WK_placebo_11_020	SA090871	FL013097	3WK	Time point
3WK_placebo_11_020	SA090871	FL013097	IBD	Status
3WK_placebo_11_020	SA090871	FL013097	prednisone	Treatment

Collection:

Collection ID:	CO001309
Collection Summary:	Stool samples were collected from all dogs before initiating therapy with prednisone, after 3 and 8 weeks, and more than one year after beginning treatment. Thirteen healthy dogs were enrolled in the study as a control group. Stool samples were kept frozen at -80oC until DNA extraction.
Sample Type:	Feces
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001330
Treatment Summary:	Thirteen dogs diagnosed with idiopathic IBD, that previously failed to respond to treatment with elimination diets and metronidazole, were enrolled. All dogs were treated with prednisone for 8 weeks. Healthy dogs enrolled as controls did not receive any treatment.

Sample Preparation:

Sampleprep ID:	SP001323
Sampleprep Summary:	Fecal samples were lyophilized and approximately 10 mg was sent to the West Coast Metabolomics Center (WCMC) at University of California at Davis (http://metabolomics.ucdavis.edu/). Samples were analyzed on a gas chromatography time-of-flight mass spectrometry (GC–TOF–MS) platform, in accordance with published methods. Briefly, samples underwent homogenization and extraction, followed by centrifugation. Dried supernatant was resuspended in methanol/chloroform and internal standards were added, followed by drying and derivatization by methoxyamine hydrochloride and N-methyl-N-trimethylsilyltrifluoroacetamide. A volume of 0.5 μL was injected in splitless mode onto a Restek rtx5SilMS column on a temperature-gradient programmed GC (oven 50–330 °C at 20 °C/min, injector 50–250 °C at 12 °C/ sec) coupled with a Leco Pegasus IV mass spectrometer (scanning 70 spectra/sec from 80 to 500 Da, −70 eV ionization energy, 1800 V detector voltage) with helium carrier gas (1 mL/min). Raw data files were processed using ChromaTOF v. 2.32. BinBase algorithm matched spectra to database compounds, and quantification was reported by peak height of an ion at the specific retention index characteristic of the compound across all samples. Peak heights were normalized by average total peak-sums for identified compounds across each sample group.

Sampleprep ID:

SP001323

Sampleprep Summary:

Fecal samples were lyophilized and approximately 10 mg was sent to the West Coast Metabolomics Center (WCMC) at University of California at Davis (http://metabolomics.ucdavis.edu/). Samples were analyzed on a gas chromatography time-of-flight mass spectrometry (GC–TOF–MS) platform, in accordance with published methods. Briefly, samples underwent homogenization and extraction, followed by centrifugation. Dried supernatant was resuspended in methanol/chloroform and internal standards were added, followed by drying and derivatization by methoxyamine hydrochloride and N-methyl-N-trimethylsilyltrifluoroacetamide. A volume of 0.5 μL was injected in splitless mode onto a Restek rtx5SilMS column on a temperature-gradient programmed GC (oven 50–330 °C at 20 °C/min, injector 50–250 °C at 12 °C/ sec) coupled with a Leco Pegasus IV mass spectrometer (scanning 70 spectra/sec from 80 to 500 Da, −70 eV ionization energy, 1800 V detector voltage) with helium carrier gas (1 mL/min). Raw data files were processed using ChromaTOF v. 2.32. BinBase algorithm matched spectra to database compounds, and quantification was reported by peak height of an ion at the specific retention index characteristic of the compound across all samples. Peak heights were normalized by average total peak-sums for identified compounds across each sample group.

Combined analysis:

Analysis ID	AN002071
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 6890N
Column	Restek Rtx-5Sil (30m x 0.25mm,0.25um)
MS Type	EI
MS instrument type	GC-TOF
MS instrument name	Leco Pegasus IV TOF
Ion Mode	POSITIVE
Units	peak area

Chromatography:

Chromatography ID:	CH001508
Instrument Name:	Agilent 6890N
Column Name:	Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:	GC

MS:

MS ID:	MS001922
Analysis ID:	AN002071
Instrument Name:	Leco Pegasus IV TOF
Instrument Type:	GC-TOF
MS Type:	EI
MS Comments:	Raw data files are preprocessed directly after data acquisition and stored as ChromaTOF-specific .peg files, as generic .txt result files and additionally as generic ANDI MS .cdf files. ChromaTOF vs. 2.32 is used for data preprocessing without smoothing, 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise levels of 5:1 throughout the chromatogram. Apex masses are reported for use in the BinBase algorithm. Result .txt files are exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics BinBase database.
Ion Mode:	POSITIVE