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MB Sample ID: SA042804
| Local Sample ID: | 17627 |
| Subject ID: | SU000807 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000807 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 17627 | SA042804 | FL008918 | Cancer | Diagnosis |
| 17627 | SA042804 | FL008918 | EA | Race |
Collection:
| Collection ID: | CO000801 |
| Collection Summary: | Frozen pathologically-verified prostate tissues were collected and stored at -140°C until analysis |
| Sample Type: | Prostate |
Treatment:
| Treatment ID: | TR000821 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP000814 |
| Sampleprep Summary: | For extraction of metabolome, 10 mg of tissue was homogenized in 1:4 ice cold water:methanol mixture containing equimolar mixture of 11 standard compounds [Epibrassinolide, [D3] Testosterone (mass difference from endogenous Testosterone = 3 Da), [15N] Anthranilic acid (mass difference from endogenous Anthranilic acid =1 Da), Zeatine, Jasmonic acid, Gibberelic acid, [D4] Estrone (mass difference from endogenous Estrone =4 Da), [15N]-Tryptophan (mass difference from endogenous Tryptophan =1 Da), [D4] Thymine (mass difference from endogenous Thymine =4 Da), [13C] Creatinine (mass difference from endogenous Creatinine =1 Da) and [15N] Arginine (mass difference from endogenous Arginine =1 Da)]. This was followed by sequential addition of ice cold chloroform and water in 3:1 ratio and separation of the organic (methanol and chloroform) and aqueous solvents (water:methanol:chloroform:water; ratio 1:4:3:1). The aqueous extract was de-proteinized using a 3 KDa molecular filter (Amicon Ultracel -3K Membrane, Millipore Corporation, Billerica, MA) and the filtrate containing metabolites was dried under vacuum (Genevac EZ-2plus, Gardiner, NY). Prior to mass spectrometry, the dried extract was resuspended in identical volume of injection solvent composed of water:methanol (50:50) and subjected to liquid chromatography (LC) mass spectrometry. |
Combined analysis:
| Analysis ID | AN001240 | AN001241 | AN001242 | AN001243 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | HILIC | HILIC |
| Chromatography system | Agilent 1290 Infinity | Agilent 1290 Infinity | Agilent 1290 Infinity | Agilent 1290 Infinity |
| Column | Waters XBridge Amide (100 x 4.6mm,3.5um) | Waters XBridge Amide (100 x 4.6mm,3.5um) | Phenomenex Luna NH2 (150 x 2.1mm,3um) | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | Agilent 6490A QQQ | Agilent 6490A QQQ | Agilent 6490A QQQ | Agilent 6490A QQQ |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | log transform with internal standard normalization | log transform with internal standard normalization | log transform with internal standard normalization | log transform with internal standard normalization |
Chromatography:
| Chromatography ID: | CH000867 |
| Chromatography Summary: | Flow rate was 0.3ml/min. Gradients were run starting from 85% buffer B (0.1% formic acid in acetonitrile) to 35% B from 0–3.5 minutes; 35% B to 2% B from 3.5–11.5 minutes; 2% B was held from 11.5–16.5 minutes; 2% B to 85% B from 16.5–17.5 minutes; 85% B was held for 7 minutes to re-equilibrate the column. |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Waters XBridge Amide (100 x 4.6mm,3.5um) |
| Flow Rate: | 0.3ml/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH000868 |
| Chromatography Summary: | Flow rate was 0.3ml/min. Gradients were run starting from 85% buffer B (HPLC grade acetonitrile ) to 35% B from 0–3.5 minutes; 35% B to 2% B from 3.5–11.5 minutes; 2% B was held from 11.5–16.5 minutes; 2% B to 85% B from 16.5–17.5 minutes; 85% B was held for 7 minutes to re-equilibrate the column |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
| Flow Rate: | 0.3ml/min |
| Solvent A: | 100% water; 20 mM ammonium formate, pH 9 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001134 |
| Analysis ID: | AN001240 |
| Instrument Name: | Agilent 6490A QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| MS ID: | MS001135 |
| Analysis ID: | AN001241 |
| Instrument Name: | Agilent 6490A QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001136 |
| Analysis ID: | AN001242 |
| Instrument Name: | Agilent 6490A QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| MS ID: | MS001137 |
| Analysis ID: | AN001243 |
| Instrument Name: | Agilent 6490A QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
