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MB Sample ID: SA053668
| Local Sample ID: | Lipkin108_negCSH_DPCSF2710_064.d |
| Subject ID: | SU000950 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000950 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Lipkin108_negCSH_DPCSF2710_064.d | SA053668 | FL010070 | ND | Diagnosis |
| Lipkin108_negCSH_DPCSF2710_064.d | SA053668 | FL010070 | FEMALE | Sex |
Collection:
| Collection ID: | CO000944 |
| Collection Summary: | CSF samples obtained from lumbar punctures were retrieved from bio-repositories at Sierra Internal Medicine (SIM) and Wisconsin Viral Research Group (WVRG). These biobank specimens were collected over time and maintained at -80°C. |
| Sample Type: | CSF |
Treatment:
| Treatment ID: | TR000964 |
| Treatment Summary: | 3 groups: 32 ME/CFS cases (11 men, 21 women) 59 comparator/control subjects (18 men, 41 women), including: 40 subjects with multiple sclerosis (MS) 19 subjects with non-infectious/non-inflammatory conditions (ND) |
Sample Preparation:
| Sampleprep ID: | SP000957 |
| Sampleprep Summary: | 1) Thaw each 100 μL CSF aliquot at room temperature (see Aliquoting TEDDY samples SOP). Once thawed (~10min) place CSF plasma samples on ice. 2) Add 225 μL cold “MeOH with QC mix” (see SOP “QC mix for LC-MS lipid analysis”). Keep MeOH on ice during extraction 3) Vortex each sample for 10s, keeping the rest on ice during all the extraction. 4) Add 750 μL of cold MTBE with 22:1 CE, keep MTBE on ice during extraction 5) Vortex for 10s 6) Shake for 6min at 4°C in the orbital mixer. 7) Add 188 μL room temperature LC/MS grade water. 8) Vortex for 20 s 9) Centrifuge for 2 min @ 14,000 rcf (12300 rpm) 10) Remove supernatant (upper phase), splitting into two aliquots of 300 μL, keeping one at –20°C for backup 11) Dry samples to complete dryness in the speed vacuum concentration system |
Combined analysis:
| Analysis ID | AN001482 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 6530 |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6530 QTOF |
| Ion Mode | NEGATIVE |
| Units | Counts |
Chromatography:
| Chromatography ID: | CH001040 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6530 |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99% B |
| Flow Rate: | 0.6 mL/min |
| Injection Temperature: | 4 C |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 5.0 uL |
| Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 eV |
| Oven Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min |
| Time Program: | 15 min |
| Washing Buffer: | Ethyl Acetate |
| Weak Wash Solvent Name: | Isopropanol |
| Strong Wash Solvent Name: | Isopropanol |
| Target Sample Temperature: | Autosampler temp 4 C |
| Sample Loop Size: | 30 m length x 0.25 mm internal diameter |
| Randomization Order: | Excel generated |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001366 |
| Analysis ID: | AN001482 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 eV |
| Collision Energy: | 40 eV |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 13 L/min |
| Dry Gas Temp: | 200 C |
| Fragment Voltage: | 175 eV |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 C |
| Ion Spray Voltage: | 1000 |
| Ionization: | Neg |
| Mass Accuracy: | Accurate |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 L/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 eV |
| Resolution Setting: | Extended Dyamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
