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MB Sample ID: SA101067
| Local Sample ID: | blank2 |
| Subject ID: | SU001458 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001458 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| blank2 | SA101067 | FL014215 | Blank | Genotype |
Collection:
| Collection ID: | CO001453 |
| Collection Summary: | 2 mL venous blood was drawn of RDT+ individuals tested at the end of the dry season (May 2012) cross-sectional, and at the first malaria episode of the ensuing transmission season, into EDTA tubes (Vacutainer K3EDTA Tubes, BD) and processed directly at the field site. Plasma (used for metabolomic analysis) was separated by centrifugation and immediately frozen in liquid N2. Buffy coat was discarded and the RBC pellet was further removed of leucocytes in a two-step procedure; first by density gradient on Lymphoprep solution (Fresenius Kabi), followed by Plasmodipur (EuroProxima) filtration. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR001473 |
| Treatment Summary: | None, samples were collected at 2 natural timepoints. RDT+ individuals tested at the end of the dry season (May 2012) cross-sectional, and at the first malaria episode of the ensuing transmission season. |
Sample Preparation:
| Sampleprep ID: | SP001466 |
| Sampleprep Summary: | Each plasma sample was split into two independent samples for metabolite extraction. For hydrophilic metabolites, 50µL of plasma was extracted by the addition of 9X volumes of ice cold methanol. Samples were briefly vortexed before centrifuging for 10 minutes to remove precipitated protein. The clarified supernatants were dried under nitrogen gas and resuspended in 100µL (1:2 dilution final). For hydrophobic metabolites, 25µL of plasma was extracted by the addition of 3X volumes of isopropanol. Samples were briefly vortexed and allowed to sit at room temperature for 10 minutes. Samples were then placed at -20 °C to precipitate overnight. Precipitated samples were centrifuged for 20 minutes and the clarified supernatant was diluted to 50% water in a glass LCMS sample vial (1:6 dilution final). Sample groups were pooled to create a group QA and all samples were pooled to create a batch QC, which were injected periodically throughout each run. |
Combined analysis:
| Analysis ID | AN002308 | AN002309 | AN002310 | AN002311 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | Reversed phase |
| Chromatography system | Shimadzu Prominence 20 UFLCXR | Thermo Dionex Ultimate 3000 | Shimadzu Prominence 20 UFLCXR | Shimadzu Prominence 20 UFLCXR |
| Column | Waters BEH C18 (100mm x 2.1mm; 1.7um) | Waters XSelect HSS T3 (100 x 2.1mm,2.5um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | QTOF | Orbitrap | QTOF | QTOF |
| MS instrument name | ABI Sciex 5600 TripleTOF | Thermo Exactive Plus Orbitrap | ABI Sciex 5600 TripleTOF | ABI Sciex 5600 TripleTOF |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Area | Area | Area |
Chromatography:
| Chromatography ID: | CH001695 |
| Instrument Name: | Shimadzu Prominence 20 UFLCXR |
| Column Name: | Waters BEH C18 (100mm x 2.1mm; 1.7um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001696 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters XSelect HSS T3 (100 x 2.1mm,2.5um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001697 |
| Instrument Name: | Shimadzu Prominence 20 UFLCXR |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001698 |
| Instrument Name: | Shimadzu Prominence 20 UFLCXR |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002151 |
| Analysis ID: | AN002308 |
| Instrument Name: | ABI Sciex 5600 TripleTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The capillary voltage was set at 4.5 kV in negative ion mode, with a declustering potential of 80V. The mass spectrometer was operated in IDA (Information Dependent Acquisition) mode with a 100 ms survey scan from 100 to 1200 m/z, and up to 20 MS/MS product ion scans (100 ms) per duty cycle using a collision energy of 50V with a 20V spread. Data processing was performed using MS-DIAL and annotated using the built-in public library. Blank subtraction and analysis was performed in excel. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002152 |
| Analysis ID: | AN002309 |
| Instrument Name: | Thermo Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Aquired in MS1 mode only. Data processing and annotation performed using MAVEN and an in-house targeted list. Blank subtraction and analysis was performed in excel. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002153 |
| Analysis ID: | AN002310 |
| Instrument Name: | ABI Sciex 5600 TripleTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | IDA MS2 method. Ammonium formate and formic acid were added to the positive ESI solvents. Data processing performed using MS-DIAL and annotated using the in silico library. Blank subtraction and analysis was performed in excel. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002154 |
| Analysis ID: | AN002311 |
| Instrument Name: | ABI Sciex 5600 TripleTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | IDA MS2 method. Ammonium acetate was used for negative ESI solvents. Data processing performed using MS-DIAL and annotated using the in silico library. Blank subtraction and analysis was performed in excel. |
| Ion Mode: | NEGATIVE |
