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MB Sample ID: SA001985
| Local Sample ID: | Group1_1 |
| Subject ID: | SU000065 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000065 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Group1_1 | SA001985 | FL000624 | AD | Cognitive Status |
Collection:
| Collection ID: | CO000048 |
| Collection Summary: | CSF was collected from individuals in the fasting state by a lumbar puncture while lying on their side or in a seated position. |
| Sample Type: | CSF |
| Collection Location: | Lumbar puncture |
Treatment:
| Treatment ID: | TR000066 |
Sample Preparation:
| Sampleprep ID: | SP000061 |
| Sampleprep Summary: | The metabolite extraction method was performed as described previously [PMID: 22415876] with minor modifications in the method. Plasma and CSF samples (100 µL) were thawed on ice at 4°C followed by deproteinization with methanol (1:4 ratio of plasma to methanol) and vortexed for 10 s, followed by incubation at −20°C for 2 h. Prior to deproteinization, 4 µL of an internal standard solution of 13C6-Phenylalanine (247 ng/µL) was added to each plasma, CSF, and quality control (QC) samples to monitor the recovery of extracted metabolites. The samples were centrifuged at 18000 g for 20 min at 4°C. The supernatants were lyophilized (Savant, Holbrook, NY) and stored at −20°C prior to analysis. The samples were reconstituted in running buffer and analyzed within 24 hrs. |
Combined analysis:
| Analysis ID | AN000080 | AN000081 | AN000082 | AN000083 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | HILIC | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) | Waters high-strength silica (150 x 2.1mm,1.8um) | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | TOF | TOF | TOF | TOF |
| MS instrument name | Agilent 6220 TOF | Agilent 6220 TOF | Agilent 6220 TOF | Agilent 6220 TOF |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Raw MS Intensities | Raw MS Intensities | Raw MS Intensities | Raw MS Intensities |
Chromatography:
| Chromatography ID: | CH000051 |
| Chromatography Summary: | C18 |
| Chromatography Comments: | Metabolite separation in plasma and CSF was achieved using an Acquity UPLC system (Waters, Milford, MA) with both hydrophilic interaction chromatography (HILIC) (ethylene-bridged hybrid 2.1150 mm, 1.7 mm; Waters) and reversed-phase liquid chromatography C18 (RPLC) (high-strength silica 2.1150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a flow rate of 400 L/min. Reverse-phase chromatography was performed using 99% solvent A (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B (95% acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. The hydrophilic interaction chromatography gradient was as follows: 0 min, 100% B; 1 min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and 20 min, 100% B. The injection volume of each sample was 5 L and column was maintained at 50C. Each sample was injected and analyzed in duplicate. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters high-strength silica (150 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH000052 |
| Chromatography Summary: | HILIC |
| Chromatography Comments: | Metabolite separation in plasma and CSF was achieved using an Acquity UPLC system (Waters, Milford, MA) with both hydrophilic interaction chromatography (HILIC) (ethylene-bridged hybrid 2.1150 mm, 1.7 mm; Waters) and reversed-phase liquid chromatography C18 (RPLC) (high-strength silica 2.1150 mm, 1.8 m; Waters). For each column, the run time was 20 min at a flow rate of 400 L/min. Reverse-phase chromatography was performed using 99% solvent A (5 mmol/L NH4 acetate, 0.1% formic acid, and 1% acetonitrile) to 100% solvent B (95% acetonitrile with 0.1% formic acid). The gradient was 0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B. The hydrophilic interaction chromatography gradient was as follows: 0 min, 100% B; 1 min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and 20 min, 100% B. The injection volume of each sample was 5 L and column was maintained at 50C. Each sample was injected and analyzed in duplicate. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ethylene-bridged hybrid (150 x 2.1mm,1.7um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS000061 |
| Analysis ID: | AN000080 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Positive-ion mode/C18: A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50-1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | POSITIVE |
| MS ID: | MS000062 |
| Analysis ID: | AN000081 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Positive-ion mode/HILIC: A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50-1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | POSITIVE |
| MS ID: | MS000063 |
| Analysis ID: | AN000082 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Negative-ion mode/C18: A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50-1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS000064 |
| Analysis ID: | AN000083 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Negative-ion mode/HILIC: A 6220 ToF-MS (Agilent Technologies) was operated in both positive and negative electrospray ionization (ESI) modes using a scan range of 50-1,200 m/z. The mass accuracy and mass resolution were 5 parts per million (ppm) and 20,000 ppm, respectively. The instrument settings were as follows: nebulizer gas temperature 325°C, capillary voltage 3.5 kV, capillary temperature 300°C, fragmentor voltage 150 V, skimmer voltage 58 V, octapole voltage 250 V, cycle time 0.5 s, and run time 15.0 min. |
| Ion Mode: | NEGATIVE |
