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MB Sample ID: SA256889
| Local Sample ID: | OUHSCPD-44 |
| Subject ID: | SU002656 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
| Cell Biosource Or Supplier: | SNU3297 and SNU3298, and patient-derived ovarian cancer cells, A#5, A#8, A#39 were from Seoul National University, Seoul, South Korea. Patient-derived ovarian cancer cells, ASC110515, ASC102315, ASC061616, ASC060915, ASC062915B and ASC011215 were from Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. |
| Cell Passage Number: | 3 to 5 |
| Cell Counts: | 20 million cells |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002656 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
| Cell Biosource Or Supplier: | SNU3297 and SNU3298, and patient-derived ovarian cancer cells, A#5, A#8, A#39 were from Seoul National University, Seoul, South Korea. Patient-derived ovarian cancer cells, ASC110515, ASC102315, ASC061616, ASC060915, ASC062915B and ASC011215 were from Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. |
| Cell Passage Number: | 3 to 5 |
| Cell Counts: | 20 million cells |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| OUHSCPD-44 | SA256889 | FL032787 | SNU-PDOCC (Cancer) | Genotype |
Collection:
| Collection ID: | CO002649 |
| Collection Summary: | Immortalized normal fallopian-tube-derived epithelial (FTE) cells, FTE188 were maintained in MCDB105: M199 (1:1) medium (Thermo Fisher Scientific, Waltham, MA), SNU3297 and SNU3298 were maintained in DMEM/F12 medium (Thermo Fisher Scientific, Waltham, MA). Patient-derived ovarian cancer cells isolated at Stephenson Cancer Center (SCC-PDOCC), ASC110515, ASC102315, ASC061616, ASC060915, ASC062915B and ASC011215, were maintained in MCDB105: DMEM (1:1) medium (Thermo Fisher Scientific, Waltham, MA). Patient-derived ovarian cancer cells isolated from Seoul National University (SNU-PDOCC), A#5, A#8, A#39 were maintained in DMEM/F12 medium. All cells were maintained at 37°C in a 5% CO2 incubator. All media were supplemented with 10% FBS (Gemini Bio-Products, West Sacramento, CA), 50 U/mL penicillin, 50 μg/ml streptomycin (Cellgro, Manassas, VA). Cells were grown to 20 million cells and washed with cold PBS. Cells were collected by scraping them off the plates. |
| Sample Type: | Cultured cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002668 |
| Treatment Summary: | No treatment was done. |
Sample Preparation:
| Sampleprep ID: | SP002662 |
| Sampleprep Summary: | Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. In order to dissociate small molecules bound to or trapped in proteins, lysate was precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis. |
Combined analysis:
| Analysis ID | AN004207 | AN004208 | AN004209 | AN004210 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Fold change over standard | Fold change over standard | Fold change over standard | Fold change over standard |
Chromatography:
| Chromatography ID: | CH003118 |
| Chromatography Summary: | Low pH polar (Metabolon). All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Raw data files are archived and extracted as described below. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 |
| Solvent B: | 0.1% formic acid and 0.05% PFPA in methanol, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003119 |
| Chromatography Summary: | Low pH Lipophilic (Metabolon). All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Raw data files are archived and extracted as described below. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 |
| Solvent B: | 0.1% formic acid and 0.05% PFPA in 50% methanol/50% acetonitrile, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003120 |
| Chromatography Summary: | High pH (Metabolon). All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Raw data files are archived and extracted as described below. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99%B in 0.5 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 6.5 mM ammonium bicarbonate in water, pH 8 |
| Solvent B: | 6.5 mM ammonium bicarbonate in 95% methanol/5% water |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003121 |
| Chromatography Summary: | HILIC (Metabolon). All methods utilized a Waters ACQUITY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 mass resolution. The sample extract was dried then reconstituted in solvents compatible to each of the four methods. Each reconstitution solvent contained a series of standards at fixed concentrations to ensure injection and chromatographic consistency. One aliquot was analyzed using acidic positive ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was also analyzed using acidic positive ion conditions, however it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient eluted from the same afore mentioned C18 column using methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and was operated at an overall higher organic content. Another aliquot was analyzed using basic negative ion optimized conditions using a separate dedicated C18 column. The basic extracts were gradient eluted from the column using methanol and water, however with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed via negative ionization following elution from a HILIC column (Waters UPLC BEH Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and data-dependent MSn scans using dynamic exclusion. The scan range varied slighted between methods but covered 70-1000 m/z. Raw data files are archived and extracted as described below. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes. |
| Flow Rate: | 0.50 mL/min |
| Solvent A: | 10 mM ammonium formate in 15% water/5% methanol/ 80% acetonitrile (effective pH 10.16 with NH4OH) |
| Solvent B: | 10 mM ammonium formate in 50% water/50% acetonitrile (effective pH 10.60 with NH4OH) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003954 |
| Analysis ID: | AN004207 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | A detailed description of data processing including chromatographic alignment, QC practices, and compound identification has been described previously (PMID: 19624122, 20955607, 30242936). Missing values, if any, were imputed with the minimum observed value for each compound and the resulting data was median scaled. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003955 |
| Analysis ID: | AN004208 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | A detailed description of data processing including chromatographic alignment, QC practices, and compound identification has been described previously (PMID: 19624122, 20955607, 30242936). Missing values, if any, were imputed with the minimum observed value for each compound and the resulting data was median scaled. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003956 |
| Analysis ID: | AN004209 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | A detailed description of data processing including chromatographic alignment, QC practices, and compound identification has been described previously (PMID: 19624122, 20955607, 30242936). Missing values, if any, were imputed with the minimum observed value for each compound and the resulting data was median scaled. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS003957 |
| Analysis ID: | AN004210 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | A detailed description of data processing including chromatographic alignment, QC practices, and compound identification has been described previously (PMID: 19624122, 20955607, 30242936). Missing values, if any, were imputed with the minimum observed value for each compound and the resulting data was median scaled. |
| Ion Mode: | NEGATIVE |
