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MB Sample ID: SA114852
| Local Sample ID: | PL25_HA_45728 |
| Subject ID: | SU001482 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001482 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| PL25_HA_45728 | SA114852 | FL014404 | AS participant | AS participant |
Collection:
| Collection ID: | CO001477 |
| Collection Summary: | Patients in this prospective clinical cohort included men diagnosed with localized prostate cancer and enrolled on an AS trial protocol between February 2006 and February 2014 (n=825). Of these, 616 patients had at least 1 year follow-up and 491 patients had baseline plasma samples, enabling inclusion in the study. The surveillance protocol was conducted by a multidisciplinary team of urologists, radiation oncologists and medical oncologists, was approved by the Institutional Review Board, and is registered on clinicaltrials.gov (NCT00490763). EDTA was used in all plasma collections and all specimens underwent a similar number of freeze/thaw cycles prior to obtaining metabolomics data. Sample ages varied, as the study began accrual in 2006 and continued over a ten year time period. Plasma was not obtained from fasted individuals. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR001497 |
| Treatment Summary: | N/A |
Sample Preparation:
| Sampleprep ID: | SP001490 |
| Sampleprep Summary: | Plasma metabolites were extracted from pre-aliquoted EDTA plasma (10 µL) with 30µL of LCMS grade methanol (ThermoFisher) in a 96-well microplate (Eppendorf). Plates were heat sealed, vortexed for 5 min at 750 rpm, and centrifuged at 2000 × g for 10 minutes at room temperature. The supernatant (10 µL) was carefully transferred to a 96-well plate, leaving behind the precipitated protein. The supernatant was further diluted with 10 µL of 100 mM ammonium formate, pH3. For Hydrophilic Interaction Liquid Chromatography (HILIC) analysis, the samples were diluted with 60 µL LCMS grade acetonitrile (ThermoFisher), whereas samples for C18 analysis were diluted with 60 µL water (GenPure ultrapure water system, Thermofisher). Each sample solution was transferred to 384-well microplate (Eppendorf) for LCMS analysis. For lipidomics, Pre-aliquoted EDTA plasma samples (10 µL) were extracted with 30µL of LCMS grade 2-propanol (ThermoFisher) in a 96-well microplate (Eppendorf). Plates were heat sealed, vortexed for 5min at 750 rpm, and centrifuged at 2000 x g for 10 minutes at room temperature. The supernatant (10µL) was carefully transferred to a 96-well plate, leaving behind the precipitated protein. The supernatant was further diluted with 90µL of 1:3:2 100mM ammonium formate, pH3 (Fischer Scientific): acetonitrile: 2-propanol and transferred to a 384-well microplate (Eppendorf) for lipids analysis using LCMS. |
Combined analysis:
| Analysis ID | AN002352 | AN002353 | AN002354 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | HILIC | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity UPLC | Waters Acquity UPLC | Waters Acquity UPLC |
| Column | Waters Acquity UPLC BEH amide,(100 x 2.1mm,1.7um,100 Å) | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um,100 Å) | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um,100 Å) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | QTOF | QTOF | QTOF |
| MS instrument name | Waters Xevo G2-XS | Waters Xevo G2-XS | Waters Xevo G2-XS |
| Ion Mode | POSITIVE | POSITIVE | POSITIVE |
| Units | normalized ion abundance | normalized ion abundance | normalized ion abundance |
Chromatography:
| Chromatography ID: | CH001724 |
| Chromatography Summary: | Chromatographic separation was performed using HILIC (Acquity™ UPLC BEH amide, 100 Å, 1.7 µm 2.1× 100mm, Waters Corporation, Milford, U.S.A). Quaternary solvent system mobile phases were (A) 0.1% formic acid in water, (B) 0.1% formic acid in acetonitrile and (D) 100mM ammonium formate, pH 3. For HILIC separation, a starting gradient of 95% B and 5% D was increase linearly to 70% A, 25% B and 5% D over a 5min period at 0.4mL/min flow rate, followed by 1 min isocratic gradient at 100 % A at 0.4mL/min flow rate.Waters Acquity™ UPLC system with 2D column regeneration configuration |
| Instrument Name: | Waters Acquity UPLC |
| Column Name: | Waters Acquity UPLC BEH amide,(100 x 2.1mm,1.7um,100 Å) |
| Flow Gradient: | a starting gradient of 95% B and 5% D was increase linearly to 70% A, 25% B and 5% D over a 5min period followed by 1 min isocratic gradient at 100% A |
| Flow Rate: | 0.4ml/min |
| Solvent A: | 100% water; 0.1% formic acid(A), 100% acetonitrile; 0.1% formic acid(B), 100% water; 100 mM ammonium formate, pH 3(D) |
| Solvent B: | 100% water; 0.1% formic acid(A), 100% acetonitrile; 0.1% formic acid(B), 100% water; 100 mM ammonium formate, pH 3(D) |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001725 |
| Chromatography Summary: | Chromatographic separation was performed using C18 (Acquity™ UPLC HSS T3, 100 Å, 1.8 µm,, 2.1×100mm, Water Corporation, Milford, U.S.A) columns at 45°C. Quaternary solvent system mobile phases were (A) 0.1% formic acid in water, (B) 0.1% formic acid in acetonitrile and (D) 100mM ammonium formate, pH 3. For C18 separation, a chromatography gradient of was as follows: starting conditions, 100% A, with linear increase to final conditions of 5% A, 95% B followed by isocratic gradient at 95% B, 5% D for 1 min.Waters Acquity™ UPLC system with 2D column regeneration configuration |
| Instrument Name: | Waters Acquity UPLC |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um,100 Å) |
| Column Temperature: | 45 |
| Flow Gradient: | starting conditions, 100% A, with linear increase to final conditions of 5% A, 95% B followed by isocratic gradient at 95% B, 5% C for 1 min. |
| Solvent A: | 100% water; 0.1% formic acid(A); 100% acetonitrile; 0.1% formic acid(B); 100 mM ammonium formate, pH 3(C) |
| Solvent B: | 100% water; 0.1% formic acid(A); 100% acetonitrile; 0.1% formic acid(B); 100 mM ammonium formate, pH 3(C) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001726 |
| Chromatography Summary: | Chromatographic separation was performed using a C18 (Acquity™ UPLC HSS T3, 100 Å, 1.8 µm, 2.1×100mm, Water Corporation, Milford, U.S.A) column at 55°C. The mobile phases were (A) water, (B) Acetonitrile, (C) 2-propanol and (D) 500mM ammonium formate, pH 3. A starting elution gradient of 20% A, 30% B, 49% C and 1% D was increased linearly to 10% B, 89% C and 1 % D for 5.5 min, followed by isocratic elution at 10% B, 89%C and 1%D for 1.5 min and column equilibration with initial conditions for 1min. Waters Acquity™ UPLC system with 2D column regeneration configuration |
| Instrument Name: | Waters Acquity UPLC |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um,100 Å) |
| Column Temperature: | 55 |
| Flow Gradient: | A starting elution gradient of 20% A, 30% B, 49% C and 1% D was increased linearly to 10% B, 89% C and 1 % D for 5.5 min, followed by isocratic elution at 10% B, 89%C and 1%D for 1.5 min and column equilibration with initial conditions for 1min. |
| Solvent A: | 100% water(A), 100% acetonitrile(B), 100% isopropanol(C), 500 mM ammonium formate, pH 3(D) |
| Solvent B: | 100% water(A), 100% acetonitrile(B), 100% isopropanol(C), 500 mM ammonium formate, pH 3(D) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002194 |
| Analysis ID: | AN002352 |
| Instrument Name: | Waters Xevo G2-XS |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Mass spectrometry data was acquired using ‘sensitivity’ mode in positive and negative electrospray ionization mode within 50-1200 Da range. For the electrospray acquisition, the capillary voltage was set at 1.5 kV (positive), 3.0kV (negative), sample cone voltage 30V, source temperature at 120° C, cone gas flow 50 L/h and desolvation gas flow rate of 800 L/h with scan time of 0.5 sec in continuum mode. Leucine Enkephalin; 556.2771 Da (positive) and 554.2615 Da (negative) was used for lockspray correction and scans were performed at 0.5 min. The injection volume for each sample was 3µL, unless otherwise specified. The acquisition was carried out with instrument auto gain control to optimize instrument sensitivity over the samples acquisition time. LC-MS and LC-MSe data were processed using Progenesis QI (Nonlinear, Waters) and values were reported as area units. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002195 |
| Analysis ID: | AN002353 |
| Instrument Name: | Waters Xevo G2-XS |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Mass spectrometry data was acquired using ‘sensitivity’ mode in positive and negative electrospray ionization mode within 50-1200 Da range. For the electrospray acquisition, the capillary voltage was set at 1.5 kV (positive), 3.0kV (negative), sample cone voltage 30V, source temperature at 120° C, cone gas flow 50 L/h and desolvation gas flow rate of 800 L/h with scan time of 0.5 sec in continuum mode. Leucine Enkephalin; 556.2771 Da (positive) and 554.2615 Da (negative) was used for lockspray correction and scans were performed at 0.5 min. The injection volume for each sample was 3µL, unless otherwise specified. The acquisition was carried out with instrument auto gain control to optimize instrument sensitivity over the samples acquisition time. LC-MS and LC-MSe data were processed using Progenesis QI (Nonlinear, Waters) and values were reported as area units. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002196 |
| Analysis ID: | AN002354 |
| Instrument Name: | Waters Xevo G2-XS |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Mass spectrometry data was acquired using ‘sensitivity’ mode in positive and negative electrospray ionization mode within 100-2000 Da for complex lipids. For the electrospray acquisition, the capillary voltage was set at 1.5 kV (positive), 3.0kV (negative), sample cone voltage 30V, source temperature at 120° C, cone gas flow 50 L/h and desolvation gas flow rate of 800 L/h with scan time of 0.5 sec in continuum mode. Leucine Enkephalin; 556.2771 Da (positive) and 554.2615 Da (negative) was used for lockspray correction and scans were performed at 0.5 min. The injection volume for each sample was 3µL, unless otherwise specified. The acquisition was carried out with instrument auto gain control to optimize instrument sensitivity over the samples acquisition time. LC-MS and LC-MSe data were processed using Progenesis QI (Nonlinear, Waters) and values were reported as area units. |
| Ion Mode: | POSITIVE |
