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MB Sample ID: SA242810
Local Sample ID: | C31 |
Subject ID: | SU002517 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 18-65 |
Gender: | Male and female |
Human Exclusion Criteria: | HIV patients, respiratory infections beside TB, diabetes, chronic renal failure history and transplanted. individuals |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002517 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 18-65 |
Gender: | Male and female |
Human Exclusion Criteria: | HIV patients, respiratory infections beside TB, diabetes, chronic renal failure history and transplanted. individuals |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
C31 | SA242810 | FL030402 | Controls | Label |
Collection:
Collection ID: | CO002510 |
Collection Summary: | Peripheral blood samples were collected at the Vendas Novas and Almada-Seixal Pneumonologic Diagnostic Centers (CDP-). Briefly, around 7 mL of blood was collected in order to obtain 3 mL of serum. Whole blood samples were harvested using Clot Activator Tubes (Monovette Serum Gel Z – 7.5 mL, S-monovette, Sarstedt®). IGRA test (QuantiFERON®-TB Gold IT, ©QIAGEN) was used to confirm infection status in Control and Latent groups. These samples were transported at 4°C to the National Institute of Health Doctor Ricardo Jorge (INSA). Samples displaying hemolysis or with unidentified IGRA results were excluded from further analysis. |
Sample Type: | Blood (serum) |
Treatment:
Treatment ID: | TR002529 |
Treatment Summary: | Blood was allowed to clot for three hours at 4°C after collection. The blood was then centrifuged at 1000 xg at 4°C for 30 min. Serum collected after centrifugation was passed through 0.2 μm filters (Sterile Acrodisc®, syringe filters with Supor membrane, 32 mm) to remove bacteria. Finally, an anti-protease cocktail (Protease Inhibitor Cocktail, ©SIGMA) was added to the filtered serum. The samples were transported from INSA to ITQB in a liquid nitrogen container and stored at −80°C. |
Sample Preparation:
Sampleprep ID: | SP002523 |
Sampleprep Summary: | Serum samples (100 µL) were extracted with 300 µL of methanol overnight at 4°C. The morning after, the samples were centrifuged for 5 min at 16.000 ×g and 4°C. The supernatant was transferred to a new tube, evaporated in the speedvac, and the pellet was stored at −20°C until further analysis. Previous to LC-MS/MS analysis the pellets were resuspended in 99.16 µL of H2O 0.1%FA. The Internal Standard (IS) – 3-Nitro-L-tyrosine – was added to a final concentration of 42 µM. In addition, four pools of samples were used for metabolite identification. |
Combined analysis:
Analysis ID | AN003951 | AN003952 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Dionex UltiMate 3000 UHPLC | Dionex UltiMate 3000 UHPLC |
Column | Waters XBridge C18 (50 x 2.1mm, 3um) | Waters XBridge C18 (50 x 2.1mm, 3um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Focus | Thermo Q Exactive Focus |
Ion Mode | POSITIVE | NEGATIVE |
Units | ua | au |
Chromatography:
Chromatography ID: | CH002925 |
Instrument Name: | Dionex UltiMate 3000 UHPLC |
Column Name: | Waters XBridge C18 (50 x 2.1mm, 3um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003686 |
Analysis ID: | AN003951 |
Instrument Name: | Thermo Q Exactive Focus |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Full-MS scan spectra were acquired in the m/z range 75 – 1125, at a resolution of 70,000 (full width at half maximum (FWHM) at m/z 200) and 1×106 automatic gain control (AGC). MS/MS scan spectra were acquired at 17,500 resolution (FWHM at m/z 200), with 1×105 AGC, maximum injection time of 100 ms and dynamic exclusion of 6 s. Raw data files were independently processed by Compound Discoverer™ 3.1 (ThermoFisher Scientific) software for metabolomics data analysis. The preferred database used for metabolite identification was mzCloud – since the "Search mzCloud '' node searches this database for matching fragmentation spectra (MS2) – followed by ChemSpider. For both databases the mass tolerance that the software used to search for matching mass peaks was set at 3 ppm. In the case of the mzCloud search the parameter "FT Fragment Mass Tolerance"was set to 5 ppm. The Human Metabolome Database (HMDB) was selected as the primary source for the ChemSpider search. |
Ion Mode: | POSITIVE |
MS ID: | MS003687 |
Analysis ID: | AN003952 |
Instrument Name: | Thermo Q Exactive Focus |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Full-MS scan spectra were acquired in the m/z range 75 – 1125, at a resolution of 70,000 (full width at half maximum (FWHM) at m/z 200) and 1×106 automatic gain control (AGC). MS/MS scan spectra were acquired at 17,500 resolution (FWHM at m/z 200), with 1×105 AGC, maximum injection time of 100 ms and dynamic exclusion of 6 s. Raw data files were independently processed by Compound Discoverer™ 3.1 (ThermoFisher Scientific) software for metabolomics data analysis. The preferred database used for metabolite identification was mzCloud – since the "Search mzCloud '' node searches this database for matching fragmentation spectra (MS2) – followed by ChemSpider. For both databases the mass tolerance that the software used to search for matching mass peaks was set at 3 ppm. In the case of the mzCloud search the parameter "FT Fragment Mass Tolerance"was set to 5 ppm. The Human Metabolome Database (HMDB) was selected as the primary source for the ChemSpider search. |
Ion Mode: | NEGATIVE |