Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA340636

Local Sample ID:	VM66_Adjacent_Kidney
Subject ID:	SU003260
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

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Subject:

Subject ID:	SU003260
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
VM66_Adjacent_Kidney	SA340636	FL040287	Adjacent_Kidney	Sample source
VM66_Adjacent_Kidney	SA340636	FL040287	-	Diagnosis

Collection:

Collection ID:	CO003253
Collection Summary:	Human tissues were collected under clinical trials approved and monitored by the Institutional Review Board (IRB) at the University of Texas Southwestern Medical Center. Tissues were collected after surgery, flash frozen in liquid nitrogen, and stored in a -80 freezer.
Sample Type:	Tissue
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003269
Treatment Summary:	Not applicable.

Sample Preparation:

Sampleprep ID:	SP003267
Sampleprep Summary:	Frozen tissue fragments weighing 10-30mg were added to ice cold 80:20 methanol:water and extracted for metabolomics analysis. Samples were subjected to three freeze-thaw cycles, then centrifuged at 16,000xg for 20 minutes to precipitate macromolecules. The supernatant was evaporated using a vacuum concentrator. Samples were resuspended in 100 μL of 0.1% formic acid in water, vortexed for 30 seconds, and centrifuged at 16,000g for 15 minutes. Supernatant was transferred to an autosampler vial and then run on the MS.

Sampleprep ID:

SP003267

Sampleprep Summary:

Frozen tissue fragments weighing 10-30mg were added to ice cold 80:20 methanol:water and extracted for metabolomics analysis. Samples were subjected to three freeze-thaw cycles, then centrifuged at 16,000xg for 20 minutes to precipitate macromolecules. The supernatant was evaporated using a vacuum concentrator. Samples were resuspended in 100 μL of 0.1% formic acid in water, vortexed for 30 seconds, and centrifuged at 16,000g for 15 minutes. Supernatant was transferred to an autosampler vial and then run on the MS.

Combined analysis:

Analysis ID	AN005157	AN005158
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Agilent 6550	Agilent 6550
Column	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Agilent 6550 QTOF	Agilent 6550 QTOF
Ion Mode	POSITIVE	NEGATIVE
Units	Normalized Abundance	Normalized Abundance

Chromatography:

Chromatography ID:	CH003904
Instrument Name:	Agilent 6550
Column Name:	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:	25
Flow Gradient:	0 min: 1% B; 5 min: 5% B; 15 min: 99%; 23 min: 99%; 24 min: 1%; 25 min: 1%
Flow Rate:	250 μL min-1
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004893
Analysis ID:	AN005157
Instrument Name:	Agilent 6550 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	ESI source conditions were set as follows: dry gas temperature 225 °C and flow 18 L min-1, fragmentor voltage 175 V, sheath gas temperature 350 °C and flow 12 L min-1, nozzle voltage 500 V, and capillary voltage +3500 V in positive mode and −3500 V in negative. The instrument was set to acquire over the full m/z range of 40–1700 in both modes, with the MS acquisition rate of 1 spectrum s-1 in profile format. Raw data files (.d) were processed using Profinder B.08.00 SP3 software (Agilent Technologies, CA) with an in-house database containing retention time and accurate mass information on 600 standards from Mass Spectrometry Metabolite Library (IROA Technologies, MA) which was created under the same analysis conditions. The in-house database matching parameters were: mass tolerance 10 ppm; retention time tolerance 0.5 min. Peak integration result was manually curated in Profinder for improved consistency and exported as a spreadsheet (.csv).
Ion Mode:	POSITIVE

MS ID:	MS004894
Analysis ID:	AN005158
Instrument Name:	Agilent 6550 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	ESI source conditions were set as follows: dry gas temperature 225 °C and flow 18 L min-1, fragmentor voltage 175 V, sheath gas temperature 350 °C and flow 12 L min-1, nozzle voltage 500 V, and capillary voltage +3500 V in positive mode and −3500 V in negative. The instrument was set to acquire over the full m/z range of 40–1700 in both modes, with the MS acquisition rate of 1 spectrum s-1 in profile format. Raw data files (.d) were processed using Profinder B.08.00 SP3 software (Agilent Technologies, CA) with an in-house database containing retention time and accurate mass information on 600 standards from Mass Spectrometry Metabolite Library (IROA Technologies, MA) which was created under the same analysis conditions. The in-house database matching parameters were: mass tolerance 10 ppm; retention time tolerance 0.5 min. Peak integration result was manually curated in Profinder for improved consistency and exported as a spreadsheet (.csv).
Ion Mode:	NEGATIVE