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MB Sample ID: SA295585
Local Sample ID: | SWHS0028 |
Subject ID: | SU002880 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Gender: | Female |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002880 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Gender: | Female |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
SWHS0028 | SA295585 | FL035934 | Study_sample | Subject_ID |
SWHS0028 | SA295585 | FL035934 | control | LungCancer |
Collection:
Collection ID: | CO002873 |
Collection Summary: | This case-control study was nested in a prospective Shanghai Women’s Health Study (December 28, 1996 - May 23, 2000), which has been previously described [17, 18]. Briefly, the SWHS is a population-based prospective cohort study in Shanghai, China where 74,942 women aged 40-70 years were recruited by a trained interviewer and a community health worker. The women were followed through multiple in-person interviews and self-administered questionnaires to obtain information on demographics, occupational and environmental exposures, lifestyle, dietary, and other factors, including environmental tobacco smoke (ETS) and body mass index (BMI). The participation rate was 92.7%. Cohort members are followed for cancer diagnosis through in-person follow-up surveys administered every 2–3 years and annual record linkage with the Shanghai Cancer Registry and Vital Statistics Unit. All incident lung cancer cases were eligible for the current study. All study participants provided written informed consent before being interviewed, and the study protocols were approved by the institutional review boards of all participating institutions. |
Sample Type: | Blood (plasma) |
Treatment:
Treatment ID: | TR002889 |
Treatment Summary: | Lung cancer cases were defined based on the International Classification of Diseases for Oncology, Second Edition (ICD-O-2), and included all primary malignant cancers that were coded as 80003, 80413, 80703, 81403, 82403, 82603, 84803, 85503, and 85603. Lung cancer was diagnosed between 2000-2014 (average follow-up: 7.0 years; range: 0 – 13 years). For each case of lung cancer, a never-smoking control matched on age (± 2 years) were selected. A total of 790 (395 cases-control pairs) lifetime never-smokers based on the standard definition used by the U.S. Centers for Disease Control (CDC) of adults who has never smoked, or who has smoked less than 100 cigarettes in their lifetime were included in the analysis. |
Sample Preparation:
Sampleprep ID: | SP002886 |
Sampleprep Summary: | Samples are prepared for metabolomics analysis using established methods (Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to analysis, plasma aliquots were removed from storage at -80°C and thawed on ice. Each cryotube is then vortexed briefly to ensure homogeneity, and 50 μL transferred to a clean microfuge tube. Immediately after, the plasma is treated with 100 μL of ice-cold LC-MS grade acetonitrile (Sigma Aldrich) containing 2.5 μL of internal standard solution with eight stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, plasma is then equilibrated for 30 min on ice, upon which precipitated proteins are removed by centrifuge (16.1 ×g at 4°C for 10 min). The resulting supernatant (100 μL) is removed, added to a low volume autosampler vial and maintained at 4°C until analysis (<22 h). |
Sampleprep Protocol ID: | EmoryUniversity_HRM_SP_082016_01.pdf |
Sampleprep Protocol Filename: | EmoryUniversity_HRM_SP_082016_01.pdf |
Processing Method: | Protein Precipitation with Acetonitrile |
Processing Storage Conditions: | On ice |
Combined analysis:
Analysis ID | AN004513 | AN004514 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | HILIC | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 RS | Thermo Dionex Ultimate 3000 RS |
Column | Higgins Analytical TARGA C18 (50 x 2.1mm,5um) | Waters XBridge BEH Amide (50 x 2.1mm,2.5um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
Ion Mode | POSITIVE | NEGATIVE |
Units | Peak Intensity | Peak Intensity |
Chromatography:
Chromatography ID: | CH003390 |
Chromatography Summary: | The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 μL of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C. |
Methods ID: | EmoryUniversity_HRM_DC5min_082016_01.pdf |
Instrument Name: | Thermo Dionex Ultimate 3000 RS |
Column Name: | Higgins Analytical TARGA C18 (50 x 2.1mm,5um) |
Column Temperature: | 40 |
Flow Gradient: | Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C. |
Flow Rate: | 0.35-0.4 mL/min |
Solvent A: | 100% water |
Solvent B: | 100% acetonitrile |
Chromatography Type: | HILIC |
Solvent C: | 100% water; 2% formic acid |
Chromatography ID: | CH003391 |
Chromatography Summary: | The C18 column is operated parallel to the HILIC column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of the C18 method, the MS is operated in negative ion mode and 10 μL of sample is injected onto the C18 column while the HILIC column is flushing with wash solution. Flow rate is maintained at 0.4 mL/min until 1.5 min, increased to 0.5 mL/min at 2 min and held for 3 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 10mM ammonium acetate in LC-MS grade water. Initial mobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min. |
Methods ID: | EmoryUniversity_HRM_DC5min_082016_01.pdf |
Instrument Name: | Thermo Dionex Ultimate 3000 RS |
Column Name: | Waters XBridge BEH Amide (50 x 2.1mm,2.5um) |
Column Temperature: | 40 |
Flow Gradient: | Initial mobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min. |
Flow Rate: | 0.4-0.5 mL/min |
Solvent A: | 100% water |
Solvent B: | 100% acetonitrile |
Chromatography Type: | Reversed phase |
Solvent C: | 100% water; 10 mM ammonium acetate |
MS:
MS ID: | MS004260 |
Analysis ID: | AN004513 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Data were acquired using full-scan mode in batches of 40 samples. Following analysis of all samples, peaks were extracted and aligned using 5 different parameters setting in apLCMS. The resulting 5 feature tables were merged using xMSanalyzer, triplicates were averaged, and batch corrected using COMBAT. |
Ion Mode: | POSITIVE |
Capillary Temperature: | 300 |
Ion Source Temperature: | 250 |
Spray Voltage: | +3500 |
Analysis Protocol File: | EmoryUniversity_HRM_FusionMS_082016_01.pdf |
MS ID: | MS004261 |
Analysis ID: | AN004514 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Data were acquired using full-scan mode in batches of 40 samples. Following analysis of all samples, peaks were extracted and aligned using 5 different parameters setting in apLCMS. The resulting 5 feature tables were merged using xMSanalyzer, triplicates were averaged, and batch corrected using COMBAT. |
Ion Mode: | NEGATIVE |
Capillary Temperature: | 300 |
Ion Source Temperature: | 250 |
Spray Voltage: | -4000 |
Analysis Protocol File: | EmoryUniversity_HRM_FusionMS_082016_01.pdf |