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MB Sample ID: SA208932
Local Sample ID: | 3058(3)-01_14_1_752 |
Subject ID: | SU002259 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Cell Strain Details: | MCF-7 |
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Subject:
Subject ID: | SU002259 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Cell Strain Details: | MCF-7 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
3058(3)-01_14_1_752 | SA208932 | FL025484 | 3058 | Treatment |
Collection:
Collection ID: | CO002252 |
Collection Summary: | Around 2x106 MCF-7 cells were plated per flask and then separately treated with SIMR3058 or SIMR3066 compounds for 12 hrs to perform proteomic analysis; the uniform number of cells per flask for each sample was to avoid the effect of variable cell number on the outcome of the specific experiment. A volume of 1 mL of the extraction solvent (methanol + 0.1% formic acid) was added to the cells, which quenched cellular metabolic activity. The cells were vortexed for 2 min to ensure the quantitative extraction of metabolites and stored in ice for 1 hr. After this, the insoluble cell matrices were subjected to intermittent ultrasonication using the COPLEY sonicator (QSONICA SONICATOR, USA) under 30% amplifier and for 30 seconds with an ice bath employed throughout the process. Following that, cells debris were centrifuged (15000 rpm, 10 min, -4 °C), and the supernatants were collected and processed for proteomics and metabolomics analysis. |
Sample Type: | Breast cancer cells |
Treatment:
Treatment ID: | TR002271 |
Treatment Summary: | Around 2x106 MCF-7 cells were plated per flask and then separately treated with SIMR3058 or SIMR3066 compounds for 12 hrs to perform proteomic analysis; the uniform number of cells per flask for each sample was to avoid the effect of variable cell number on the outcome of the specific experiment. A volume of 1 mL of the extraction solvent (methanol + 0.1% formic acid) was added to the cells, which quenched cellular metabolic activity. The cells were vortexed for 2 min to ensure the quantitative extraction of metabolites and stored in ice for 1 hr. After this, the insoluble cell matrices were subjected to intermittent ultrasonication using the COPLEY sonicator (QSONICA SONICATOR, USA) under 30% amplifier and for 30 seconds with an ice bath employed throughout the process. Following that, cells debris were centrifuged (15000 rpm, 10 min, -4 °C), and the supernatants were collected and processed for proteomics and metabolomics analysis. |
Sample Preparation:
Sampleprep ID: | SP002265 |
Sampleprep Summary: | Around 2x106 MCF-7 cells were plated per flask and then separately treated with SIMR3058 or SIMR3066 compounds for 12 hrs to perform proteomic analysis; the uniform number of cells per flask for each sample was to avoid the effect of variable cell number on the outcome of the specific experiment. A volume of 1 mL of the extraction solvent (methanol + 0.1% formic acid) was added to the cells, which quenched cellular metabolic activity. The cells were vortexed for 2 min to ensure the quantitative extraction of metabolites and stored in ice for 1 hr. After this, the insoluble cell matrices were subjected to intermittent ultrasonication using the COPLEY sonicator (QSONICA SONICATOR, USA) under 30% amplifier and for 30 seconds with an ice bath employed throughout the process. Following that, cells debris were centrifuged (15000 rpm, 10 min, -4 °C), and the supernatants were collected and processed for proteomics and metabolomics analysis. |
Combined analysis:
Analysis ID | AN003561 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Bruker Elute |
Column | Hamilton Intensity Solo 2 C18 |
MS Type | ESI |
MS instrument type | QTOF |
MS instrument name | Bruker timsTOF |
Ion Mode | POSITIVE |
Units | AU |
Chromatography:
Chromatography ID: | CH002632 |
Chromatography Summary: | Samples were chromatographically separated using a Hamilton® Intensity Solo 2 C18 column (100 mm x 2.1 mm x 1.8 µm) and eluted using 0.1% formic acid in water (A) and 0.1% formic acid in ACN (B) using the following gradient: at a flow rate of 0.250 ml/min 1% B from 0-2 min, then gradient elution to 99% B from 2-17 min, held at 99% B from 17-20 min, then re-equilibrated to 1% B from 20-30 min using a flow rate of 0.350 ml/min. The autosampler temperature was set at 8℃ and the column oven temperature at 35℃. |
Instrument Name: | Bruker Elute |
Column Name: | Hamilton Intensity Solo 2 C18 |
Column Temperature: | 35 |
Flow Gradient: | 1%B to 99%B in 15 min |
Flow Rate: | 250 uL/min |
Solvent A: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile; 0.1% formic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003318 |
Analysis ID: | AN003561 |
Instrument Name: | Bruker timsTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
MS Comments: | Auto MS/MS mode with 0.5 second cycle time. The ESI source with dry nitrogen gas was 10 L/min, and the drying temperature was equal to 220℃ with nebulizer gas pressure set to 2.2 bar. The capillary voltage of the ESI was 4500 V and the Plate Offset 500 V. MS acquisition scan was set from 20-1300 m/z and the collision energy to 7 eV. |
Ion Mode: | POSITIVE |