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MB Sample ID: SA351595
Local Sample ID: | UM082 |
Subject ID: | SU003329 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU003329 |
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 |
---|---|---|---|---|
UM082 | SA351595 | FL041039 | Breast Cancer Cell Line | Sample source |
UM082 | SA351595 | FL041039 | Single_cell | Sample type |
Collection:
Collection ID: | CO003322 |
Collection Summary: | Two hours before metabolite extraction, the cell culture medium was replaced with fresh medium. Single cell and cell cluster states were collected and centrifuged at 800 × g for 3 min to remove culture media. Then, the cells were resuspended in 1 mL of precooled PBS (4°C) and transferred into a 1.5 mL eppendorf tube. After removing supernatant by centrifugation at 800 × g for 3 min, the tube containing cell pellet was immediately incubated in liquid nitrogen for 1 min to quench enzyme activity and stop the degradation of metabolites. |
Collection Protocol Filename: | WZC_Collection_protocol.pdf |
Sample Type: | Cultured cells |
Treatment:
Treatment ID: | TR003338 |
Treatment Summary: | MDA-MB-231 cells and MDA-MB-453 were maintained in L-15 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37 °C in a free gas exchange with atmospheric air. |
Sample Preparation:
Sampleprep ID: | SP003336 |
Sampleprep Summary: | 300 μL of H2O was then added to the tube, and the cells were fully lysed by an ultrasonic cell disruptor for 10 min at 4°C. After mixing, 20 μL of suspension was collected for protein quantification and subsequent data normalization. Then, methanol (precooled to −80°C) was added into the tube to make 80% methanol solution (v/v). The tube was vortexed vigorously for 5 min and centrifuged at 14,000 × g for 10 min at 4°C to remove the cell debris. Afterward, the metabolite-containing supernatant was transferred to a new tube on ice. The supernatant was evaporated to dryness in a vacuum concentrator and reconstituted in 100 μL of methanol: H2O (1:1, v/v), which was centrifuged again at 14000 × g for 15 min at 4°C to remove insoluble debris. |
Sampleprep Protocol Filename: | Sampleprep_protocol.pdf |
Combined analysis:
Analysis ID | AN005262 | AN005263 | AN005264 | AN005265 |
---|---|---|---|---|
Analysis type | MS | MS | MS | MS |
Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
Column | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) |
MS Type | ESI | ESI | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
Units | Peak area | Peak area | Peak area | Peak area |
Chromatography:
Chromatography ID: | CH003983 |
Methods Filename: | Chromatography_methods.pdf |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Agilent InfinityLab Poroshell 120 HILIC-Z (100 x 2.1mm, 2.7um) |
Column Temperature: | 40 |
Flow Gradient: | 85% B (0 min) to 85% B (1 min) to 65% B (12 min) to 40% B (12.1 min) to 40% B (15 min) to 85% B (15.1 min) to 85% B (20 min), the flow gradient increases linearly between the time points mentioned. |
Flow Rate: | 0.3 mL/min |
Solvent A: | 100% Water; 25 mM Ammonium acetate; 25 mM Ammonium hydroxide |
Solvent B: | 100% Acetonitrile |
Chromatography Type: | HILIC |
Chromatography ID: | CH003984 |
Methods Filename: | Chromatography_methods.pdf |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) |
Column Temperature: | 40 |
Flow Gradient: | 10% B (0 min) to 30% B (1 min) to 95% B (19 min) to 95% B (20 min) to 10% B (20.1 min) to 10% B (23 min), the flow gradient increases linearly between the time points mentioned. |
Flow Rate: | 0.4 mL/min |
Solvent A: | 100% Water; 0.1% Formic acid |
Solvent B: | 100% Acetonitrile; 0.1% Formic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS004993 |
Analysis ID: | AN005262 |
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 |
Analysis Protocol File: | MS_analysis_protocol.pdf |
MS ID: | MS004994 |
Analysis ID: | AN005263 |
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 |
Analysis Protocol File: | MS_analysis_protocol.pdf |
MS ID: | MS004995 |
Analysis ID: | AN005264 |
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 |
Analysis Protocol File: | MS_analysis_protocol.pdf |
MS ID: | MS004996 |
Analysis ID: | AN005265 |
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 |
Analysis Protocol File: | MS_analysis_protocol.pdf |