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MB Sample ID: SA308171
| Local Sample ID: | C00544 |
| Subject ID: | SU002954 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002954 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| C00544 | SA308171 | FL037076 | 1 | Diagnosis |
Collection:
| Collection ID: | CO002947 |
| Collection Summary: | The Weill Cornell EDRN Prostate Cancer Cohort consented and recruited 1,144 patients (518 cases and 626 controls) over 9 years (from 2008 to 2017). In order to be eligible for the study, patients needed to be adult males, have no prior history of prostate cancer or prostate biopsies, and be scheduled to undergo prostate biopsy at Weill Cornell Medicine in New York City. Need of prostate biopsy was determined based on suspicion of prostate cancer, which primarily included elevated PSA levels, abnormal digital rectal exam (DRE) results, or suspicious findings based on imaging. Prostate biopsies included at least 10 cores taken in a laterally directed fashion, and a fasting blood sample was collected prior to prostate biopsy from all recruited patients. Biopsy tissue, together with urine and blood samples were processed and biobanked at Weill Cornell Medicine. For each patient, extensive clinical parameters were collected, including biopsy results, prostate cancer diagnosis and 2-year follow-up clinical information. EDTA-plasma samples for metabolomics profiling were selected to include patients with complete 12- and 24-months follow-up information available (see Data Records section for more details). This subset included a total of 580 patients, with 267 men diagnosed with PCa and 313 controls. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR002963 |
| Treatment Summary: | Fasting blood was collected prior to biopsy in 6ml BD Vacutainer® EDTA tubes. Immediately after blood draw, the tube was inverted 8-10 times to mix the additive with the blood and placed immediately on ice. Tubes were centrifuged at 2,500 rpm for 15 minutes at 4°C within two hours of blood collection. Plasma aliquots of 100ul or 200ul were extracted from the top layer, transferred into 0.5ml polypropylene micro tubes and stored at -80C until shipment for metabolomic profiling. |
Sample Preparation:
| Sampleprep ID: | SP002960 |
| Sampleprep Summary: | Following receipt, samples were inventoried and immediately stored and maintained at -80oC until processed. Each received sample was assigned a unique identifier, which was used to track all sample handling, tasks, and results. The samples and all derived aliquots were tracked throughout the process via an automated system. On the day of extraction, frozen samples were thawed on ice. Samples were prepared using the automated MicroLab STAR® system (Hamilton Company, Reno, NV). 100 µl of each sample was transferred into a well in a deepwell plate. Prior to extraction, several isotopically labelled standards were added to each sample to ensure accurate extraction of the samples. To remove proteins or dissociate small molecules bound to proteins or trapped in the precipitated protein matrix, proteins were precipitated with 500 µl of methanol under vigorous shaking for 2 minutes in a GenoGrinder 2000 (Glen Mills, Inc, Clifton, NJ) followed by centrifugation for 10 minutes at 680g. |
Combined analysis:
| Analysis ID | AN004654 | AN004655 | AN004656 | AN004657 |
|---|---|---|---|---|
| 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 UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC 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 | peak area | peak area | peak area | peak area |
Chromatography:
| Chromatography ID: | CH003503 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40-50 |
| 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: | CH003504 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes. |
| Flow Rate: | 0.60 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: | CH003505 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40-50 |
| 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: | CH003506 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 40-50 |
| 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: | MS004401 |
| Analysis ID: | AN004654 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos early). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) 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 linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | preprocessing_workflow.docx |
| MS ID: | MS004402 |
| Analysis ID: | AN004655 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos late). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) 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 linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | preprocessing_workflow.docx |
| MS ID: | MS004403 |
| Analysis ID: | AN004656 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Neg). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) 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 linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | preprocessing_workflow.docx |
| MS ID: | MS004404 |
| Analysis ID: | AN004657 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Polar). Mass spectrometry was performed using a Q-Exactive (Thermo Scientific, Waltham, MA) 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 linearity of the instrument performance standards has been shown previously. Immediately prior to analysis, dried samples were reconstituted in solvents compatible with each of the four methods, as described below. Each reconstitution solvent contained several instrument performance standards at fixed concentrations to ensure injection and chromatographic consistency, and to aid peak alignment. The injection volume was 5 mL with a 2x loop overfill. |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | preprocessing_workflow.docx |
