Return to study ST000614 main page
MB Sample ID: SA034018
Local Sample ID: | 0a15bd3c |
Subject ID: | SU000637 |
Subject Type: | Bladder Cancer Tissues |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU000637 |
Subject Type: | Bladder Cancer Tissues |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Species Group: | Human |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
0a15bd3c | SA034018 | FL007468 | Cancer | Diagonsis |
0a15bd3c | SA034018 | FL007468 | Former Smoker | Smoking Status |
Collection:
Collection ID: | CO000631 |
Collection Summary: | Witten-Herdecke University;The University of Texas Southwestern Medical Center; Baylor College of Medicin |
Sample Type: | Bladder tissue |
Treatment:
Treatment ID: | TR000651 |
Treatment Summary: | NA |
Sample Preparation:
Sampleprep ID: | SP000644 |
Sampleprep Summary: | All the tissues and urine samples used for this study were stored in -140oC. 50 mg of tissue was used for the extraction. For cell lines, 3 x106 cell pellets were thawed at 4 °C and subjected to three freeze-thaw cycles, freezing in liquid nitrogen and thawing on ice, to rupture the cell membranes. The extraction step start with 750 µL ice-cold methanol:water (4:1) containing 20 µL spiked internal standards was added to each cell pellet or tissue sample. Ice-cold chloroform and water was added in a 3:1 ratio for a final proportion of 1:4:3:1 water:methanol:chloroform:water. The organic (methanol and chloroform) and aqueous layers dried and re suspended with 50:50 methonal: water. The extract was deproteinized using a 3-kDa molecular filter (Amicon Ultracel-3K Membrane; Millipore Corporation, Billerica, MA) and the filtrate was dried under vacuum (Genevac EZ-2plus; Gardiner, Stone Ridge, NY). Prior to mass spectrometry, the dried extracts were resuspended in identical volumes of injection solvent composed of 1:1 water:methanol and subjected to liquid chromatography-mass spectrometry. 50 ul of urine was used for sample preparation. Internal standard was spiked into raw sample. Then it was processed through Amicon 3k filter. After that, 50 ul of urine sample was diluted with 450 solvent ( methanol water =50:50 v/v) and subjected to LC/MS analysis. The injection volume was 10 ul. |
Combined analysis:
Analysis ID | AN000939 | AN000940 | AN000941 | AN000942 | AN000943 |
---|---|---|---|---|---|
Analysis type | MS | MS | MS | MS | MS |
Chromatography type | HILIC | HILIC | HILIC | HILIC | HILIC |
Chromatography system | Unspecified | Unspecified | Unspecified | Unspecified | Unspecified |
Column | Waters XBridge Amide (100 x 4.6mm,3.5um) | Waters XBridge Amide (100 x 4.6mm,3.5um) | 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) |
MS Type | ESI | ESI | ESI | ESI | ESI |
MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole | Triple quadrupole | Triple quadrupole |
MS instrument name | Agilent 6495 QQQ | Agilent 6495 QQQ | Agilent 6495 QQQ | Agilent 6495 QQQ | Agilent 6495 QQQ |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | POSITIVE | POSITIVE |
Units | Peak intensity | Peak intensity | Peak intensity | Peak intensity | Peak intensity |
Chromatography:
Chromatography ID: | CH000670 |
Instrument Name: | Unspecified |
Column Name: | Waters XBridge Amide (100 x 4.6mm,3.5um) |
Chromatography Type: | HILIC |
Chromatography ID: | CH000671 |
Instrument Name: | Unspecified |
Column Name: | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
Chromatography Type: | HILIC |
MS:
MS ID: | MS000835 |
Analysis ID: | AN000939 |
Instrument Name: | Agilent 6495 QQQ |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
Ion Mode: | POSITIVE |
MS ID: | MS000836 |
Analysis ID: | AN000940 |
Instrument Name: | Agilent 6495 QQQ |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
Ion Mode: | NEGATIVE |
MS ID: | MS000837 |
Analysis ID: | AN000941 |
Instrument Name: | Agilent 6495 QQQ |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
Ion Mode: | POSITIVE |
MS ID: | MS000838 |
Analysis ID: | AN000942 |
Instrument Name: | Agilent 6495 QQQ |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
Ion Mode: | POSITIVE |
MS ID: | MS000839 |
Analysis ID: | AN000943 |
Instrument Name: | Agilent 6495 QQQ |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
Ion Mode: | POSITIVE |