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MB Sample ID: SA081174
| Local Sample ID: | S_62 |
| Subject ID: | SU001236 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 30-60 |
| Gender: | Male |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001236 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 30-60 |
| Gender: | Male |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| S_62 | SA081174 | FL012382 | [40-50) yrs | Age Group |
| S_62 | SA081174 | FL012382 | WTC-LI | Group |
Collection:
| Collection ID: | CO001230 |
| Collection Summary: | Fasting blood drawn |
| Sample Type: | Blood (serum) |
| Collection Location: | Bureau of Health Services (BHS) and the FDNY Headquarters, (9 Metrotech Center, Brooklyn, NY) |
| Collection Duration: | 6 month after 9/11/2001 and once at 2008 |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001251 |
| Treatment Summary: | No available |
Sample Preparation:
| Sampleprep ID: | SP001244 |
| Sampleprep Summary: | The Fire Department of New York City (FDNY) serum sampling occurred at the Bureau of Health Services (BHS) and the FDNY Headquarters (9 Metrotech Center, Brooklyn, NY). Serum processing and analysis occurred in the PI’s Laboratory at New York University /Bellevue. The specimens were stored in the New York University-The Fire Department of New York City- World Trade Center Lung Injury Biorepository (NYU-FDNY WTC) in Dr. Nolan’s laboratory. Each stored specimen was labeled with a unique code. This unique code on the sample was linked to a specific subject. Samples were stored in -80 oC and shipped to the Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC) on dry ice. Table 1 lists the sample ID and associated metadata provided. Serum samples were thawed at 4 °C overnight. All samples were vortexed via multiple tube vortex mixer for 2 min at 3000 rpm. Serum samples were centrifuged at 1000 rpm for 30 sec. A volume of 8 µL aliquot of each studied samples was transferred into a 10.0 mL tube to make the Study Pool (SP). A volume of 1500 µL of CHEAR Reference Plasma was used for the CHEAR Pool (CP). An aliquot of 50 µL serum (including experimental samples, SP, and CP) was transferred to a new, pre-labeled Lo-Bind Eppendorf tube. There were total 200 experimental samples, 24 SP samples, and 24 CP samples in this study. The samples were extracted by 400 µL methanol with 500 ng/ml tryptophan-d5 as internal standard via a multiple tube vortex mixer for 2 min at 5000 rpm. Protein precipitate was pelleted using a centrifuge operating at room temperature for 4 min at 16,000 rcf. A volume of 350 µl of the supernatant was transferred into a pre-labeled 2.0 ml Low-bind Eppendorf tube, and then dried by a SpeedVac overnight. For immediate analysis, 100 µL of water-methanol solution (95:5, v/v) was added to reconstitute the dried extracts, and the samples were thoroughly mixed on multiple tube vortex mixer for 10 min at 5000 rpm. Samples were centrifuged at 4°C for 4 min at 16,000 rcf. The supernatant was transferred to pre-labeled autosampler vials for data acquisition by LC-MS. Broad-spectrum metabolomics was conducted using a Thermo Scientific™ Vanquish™ UPHPLC - Q Exactive™ HF-X Orbitrap System. Metabolites were separated on an Acquity UPLC HSS T3 C18 (2.1 X 100 mm, 1.8 µm) operating at 50 C using a reversed phase gradient separation with Water with 0.1% Formic Acid (v/v) as mobile phase A and Methanol with 0.1% Formic Acid (v/v) as mobile phase B. A 5 µL was injected into the instrument, and MS was collected between 50-750 m/z in positive mode with the MS/MS data triggered by the Data-Dependent Acquisition. |
| Extraction Method: | Vortex with methanol containing 500ng/ml tryptophan-d5 as internal standard |
| Extract Storage: | -80℃ |
| Sample Resuspension: | Water-Methanol (95:5, v/v) |
| Sample Spiking: | Tryptophan-d5 |
Combined analysis:
| Analysis ID | AN001936 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH001405 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 50 |
| Flow Gradient: | Time(min) Flow Rate %A %B Curve 1. 0 0.4 99.0 1.0 5 2. 1.00 0.4 99.0 1.0 5 3. 16.00 0.4 1.0 99.0 5 4. 19.00 0.4 1.0 99.0 5 5. 19.50 0.4 99.0 1.0 5 |
| Flow Rate: | 0.4 mL/min |
| Injection Temperature: | 8 |
| Internal Standard: | Tryptophan-d5 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001792 |
| Analysis ID: | AN001936 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LC-MS/MS data was acquired by data dependent acquisition;Progenesis QI was used to process the raw data. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 275 C |
| Capillary Voltage: | 3.75 kV |
| Collision Energy: | 20, 30, 45 |
| Collision Gas: | N2 |
| Dry Gas Flow: | 45 arbitary unit |
| Dry Gas Temp: | 325 oC |
| Fragmentation Method: | CID |
| Gas Pressure: | 45 arbitary unit |
| Ion Source Temperature: | 325 oC |
| Ion Spray Voltage: | 3.75 kV |
| Ionization: | ESI |
| Ionization Potential: | positive |
| Mass Accuracy: | 5ppm |
| Source Temperature: | 325 oC |
| Spray Voltage: | 3.75 kV |
| Resolution Setting: | 120000 |
| Scan Range Moverz: | 70-1050 m/z |
| Scanning Range: | 70-1050 m/z |
