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MB Sample ID: SA235159
Local Sample ID: | SW480_neg_09 |
Subject ID: | SU002430 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002430 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
SW480_neg_09 | SA235159 | FL029177 | Low metastatic ability | Class |
Collection:
Collection ID: | CO002423 |
Collection Summary: | Two hours before metabolite extraction, the cell culture medium was replaced with fresh medium. After discarding the medium in each culture dish, the cells were quickly rinsed twice with cold isotonic saline (0.9% NaCl [w/v], 4 °C). Water (1.5 mL) was added to each dish, and then the dishes were stored in a freezer (−80 °C) for 20 min before extraction. |
Sample Type: | Cultured cells |
Treatment:
Treatment ID: | TR002442 |
Treatment Summary: | SW480 cells and SW620 cells were cultured in DMEM medium supplemented with 10% FBS at 37 °C under a 5% CO2 atmosphere, HT-29 and COLO 205 cells were cultured in RPMI 1640 medium supplemented with 10% FBS at 37 °C under a 5% CO2 atmosphere. |
Cell Media: | DMEM medium supplemented with 10% FBS is for SW480 cells and SW620 cells, while RPMI 1640 medium supplemented with 10% FBS is for HT-29 and COLO 205 cells. |
Cell Envir Cond: | at 37 °C under a 5% CO2 atmosphere |
Cell Harvesting: | After discarding the medium in each culture dish, the cells were quickly rinsed twice with cold isotonic saline (0.9% NaCl [w/v], 4 °C). Water (1.5 mL) was added to each dish, and then the dishes were stored in a freezer (−80 °C) for 20 min before extraction. Then, cells were collected by scraping with a cell scraper. |
Cell Pct Confluence: | 70%-80% |
Sample Preparation:
Sampleprep ID: | SP002436 |
Sampleprep Summary: | Cell lysates (20 μL) were removed for a protein assay, and the remaining cell lysates were extracted by the addition of 4.5 mL of methanol containing 3 μg of internal standard (acetaminophen). The cells were completely collected with a cell scraper. Finally, the suspension of cell debris in each dish was transferred to an Eppendorf tube, vigorously vortexed for 5 min, and then centrifuged at 10,000×g for 10 min at 4 °C. The supernatant was transferred to another tube and evaporated to dryness in a Refrigerated CentriVap Benchtop Vacuum Concentrator (Labconco Corporation, Kansas City, MO). The pellets were reconstituted with methanol-water (75:25) and centrifuged twice at 12,000×g for 15 min at 4 °C. |
Combined analysis:
Analysis ID | AN003824 | AN003825 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | UPLC Ultimate 3000 system | UPLC Ultimate 3000 system |
Column | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
Ion Mode | POSITIVE | NEGATIVE |
Units | Peak area | Peak area |
Chromatography:
Chromatography ID: | CH002830 |
Instrument Name: | UPLC Ultimate 3000 system |
Column Name: | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) |
Column Temperature: | 40 °C |
Flow Gradient: | 10% B (0 min) → 30% B (1 min) → 95% B (19 min) → 95% B (20 min) |
Flow Rate: | 0.4 mL/min |
Injection Temperature: | 4 °C |
Solvent A: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile; 0.1% formic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003566 |
Analysis ID: | AN003824 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | All operations and acquisitions were controlled by Xcalibur 2.0.7 (Thermo Fisher Scientific, Bremen, Germany).UPLC-HRMS data were analyzed using MS-DIAL software after conversion to mzML file format using MSConvert (Version 3.0, ProteiWizard). |
Ion Mode: | POSITIVE |
Capillary Temperature: | 300 °C |
Capillary Voltage: | +3.5 kV |
MS ID: | MS003567 |
Analysis ID: | AN003825 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | All operations and acquisitions were controlled by Xcalibur 2.0.7 (Thermo Fisher Scientific, Bremen, Germany).UPLC-HRMS data were analyzed using MS-DIAL software after conversion to mzML file format using MSConvert (Version 3.0, ProteiWizard). |
Ion Mode: | NEGATIVE |
Capillary Temperature: | 300 °C |
Capillary Voltage: | -2.5 kV |