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MB Sample ID: SA340641
Local Sample ID: | VM41_Adjacent_Kidney |
Subject ID: | SU003260 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
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 |
---|---|---|---|---|
VM41_Adjacent_Kidney | SA340641 | FL040287 | Adjacent_Kidney | Sample source |
VM41_Adjacent_Kidney | SA340641 | 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. |
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 |