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MB Sample ID: SA177796
| Local Sample ID: | CZ.0133.005_1 |
| Subject ID: | SU001996 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001996 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| CZ.0133.005_1 | SA177796 | FL021981 | 2 | Sex |
| CZ.0133.005_1 | SA177796 | FL021981 | 2 | Smoking_status |
Collection:
| Collection ID: | CO001989 |
| Collection Summary: | Identification of factories and worker enrollment are described in detail elsewhere. [14] Study subjects were enrolled in the Fall of 1992 in Shanghai, China and evaluated at the Shanghai Hygiene and Anti-Epidemic Institute. The study protocol was explained to all potential participants, and informed consent was obtained using Institutional Review Board-approved procedures. Data collected included age, gender, tobacco use, alcohol consumption, medical history, and an occupational work history. Prior to the clinical visit, study subjects were asked to refrain from eating solid foods after dinner the night before and the morning of the clinical phase of the study. The following morning, a 27 mL sample of blood was obtained by venous phlebotomy. Plasma samples were then frozen at -80°C, shipped to the NCI on dry ice, and stored continuously at -80°C until analysis. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
| Additives: | EDTA |
Treatment:
| Treatment ID: | TR002008 |
| Treatment Summary: | Details of personal benzene exposure assessment have been reported previously. [14] In brief, individual exposure was monitored by organic vapor passive dosimetry badges (3M no. 3500. St.Paul. Minnesota), which were worn by each worker for a full shift on 5 separate days for a 1–2 week period prior to blood collection. Badges were analyzed by gas chromatography (GC) with flame ionization detection for benzene, toluene, and xylene. Average exposure was calculated for each compound as the geometric mean of the five air measurements. In this study, we focus on control workers with no benzene exposure, lower (relative) exposures (<20ppm) and high exposure (>20ppm) Due to benzene levels exceeding the current OSHA time-weighted exposure limit of 1 ppma for all exposed workers, the median exposure of 20 ppm was used to classify low- and high-exposed workers to identify exposure-associated metabolic changes. For each m/z feature, peak intensity was log2 transformed to test for association with benzene across the categories of exposure, which included controls, low exposed (<20 ppma) and high exposed (≥20 ppma), defined as a continuous variable (control=0; < 20 ppma= 1; ≥20 ppma= 2) |
Sample Preparation:
| Sampleprep ID: | SP002002 |
| 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 |
| Extraction Method: | 2:1 addition of acetonitrile |
| Sample Spiking: | [13C6]-D-glucose, [15N,13C5]-L-methionine, [13C5]-L-glutamic acid, [15N]-L-tyrosine, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine, [15N]-indole |
Combined analysis:
| Analysis ID | AN003116 | AN003117 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters XBridge BEH Amide XP HILIC (50 x 2.1mm,2.5m) | Higgins endcapped C18 (50 x 2.1mm,3um) |
| 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 area | Peak area |
Chromatography:
| Chromatography ID: | CH002301 |
| Chromatography Summary: | HILIC–positive chromatography method 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 Filename: | EmoryUniversity_HRM-QEHF_DC5min_092017_v1.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters XBridge BEH Amide XP HILIC (50 x 2.1mm,2.5m) |
| 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. |
| Solvent A: | 100% water(A), 100% acetonitrile(B), 100% water; 2% formic acid(C) |
| Solvent B: | 100% water(A), 100% acetonitrile(B), 100% water; 2% formic acid(C) |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH002302 |
| Chromatography Summary: | C18–negative chromatography method 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 Filename: | EmoryUniversity_HRM-QEHF_DC5min_092017_v1.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Higgins endcapped C18 (50 x 2.1mm,3um) |
| 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. |
| Flow Rate: | 0.4 mL/min-0.5 mL/min |
| Solvent A: | 100% water(A), 100% acetonitrile(B), 10 mM ammonium acetate(C) |
| Solvent B: | 100% water(A), 100% acetonitrile(B), 10 mM ammonium acetate(C) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002897 |
| Analysis ID: | AN003116 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer was operated at a resolution of 120,000. Source tune settings were optimized using a standard mixture for both positive and negative mode, resulting in capillary temperature, vaporizer temperature, sheath gas, auxiliary gas, sweep gas and S-Lens RF level settings of 250°C, 150°C, 45 (arbitrary units), 5 (arbitrary units), 1 (arbitrary units) and 55, respectively. Positive mode ESI was operated using a spray voltage of +3.5 kV. High-resolution detection of m/z features was accomplished by maximum injection time of 100 milliseconds and AGC target of 1x106. During untargeted data acquisition, no exclusion or inclusion masses were selected, and data was acquired in MS1 mode only over the scan range of 85-1250 m/z. Following instrumental analysis of all study and quality control (QC) samples, which included NIST SRM 1950 and pooled human plasma, instrument files were converted to .mzXML format and m/z features were extracted and aligned at multiple parameter settings using apLCMS. [2] The resulting feature tables were then merged with xMSanalyzer [3], which systemically evaluates sample profile quality, feature detection and technical reliability for optimal peak selection. Only features exhibiting a median triplicate coefficient of variation ≤ 100% and detected in greater than 25% of the study samples were retained. The resulting feature table was then batch corrected using ComBat [4] and triplicate injections averaged prior to analysis. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 250 |
| Dry Gas Flow: | 45 |
| Dry Gas Temp: | 150 |
| Ion Source Temperature: | 150 |
| Analysis Protocol File: | EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf |
| MS ID: | MS002898 |
| Analysis ID: | AN003117 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer was operated at a resolution of 120,000. Source tune settings were optimized using a standard mixture for both positive and negative mode, resulting in capillary temperature, vaporizer temperature, sheath gas, auxiliary gas, sweep gas and S-Lens RF level settings of 250°C, 150°C, 45 (arbitrary units), 5 (arbitrary units), 1 (arbitrary units) and 55, respectively. Negative mode ESI was operated at -4 kV. High-resolution detection of m/z features was accomplished by maximum injection time of 100 milliseconds and AGC target of 1x106. During untargeted data acquisition, no exclusion or inclusion masses were selected, and data was acquired in MS1 mode only over the scan range of 85-1250 m/z. Following instrumental analysis of all study and quality control (QC) samples, which included NIST SRM 1950 and pooled human plasma, instrument files were converted to .mzXML format and m/z features were extracted and aligned at multiple parameter settings using apLCMS. [2] The resulting feature tables were then merged with xMSanalyzer [3], which systemically evaluates sample profile quality, feature detection and technical reliability for optimal peak selection. Only features exhibiting a median triplicate coefficient of variation ≤ 100% and detected in greater than 25% of the study samples were retained. The resulting feature table was then batch corrected using ComBat [4] and triplicate injections averaged prior to analysis. |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 250 |
| Dry Gas Flow: | 45 |
| Dry Gas Temp: | 150 |
| Ion Source Temperature: | 150 |
| Analysis Protocol File: | EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf |
