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MB Sample ID: SA305844
| Local Sample ID: | 6 |
| Subject ID: | SU002936 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002936 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 6 | SA305844 | FL036731 | ADEQUATE | Case_Control |
Collection:
| Collection ID: | CO002929 |
| Collection Summary: | Plasma samples analyzed in this study were collected from the antecubital vein in 7 mL Vacutainer® tubes containing K2-EDTA (Beckton Dickinson, Franklin Lakes, NJ, USA). |
| Collection Protocol Filename: | La_Frano_Treatment_Protocol_v1[23].pdf |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR002945 |
| Treatment Summary: | The samples for this study were obtained from archived specimens from a cross-sectional survey that assessed the prevalence of VAD among a convenience sample of 207 lactating women in the province of Santa Margarita, Samar, Philippines. The original protocol was approved by the UC Davis IRB 290430-5 and the ethical committee of the local Ministry of Health in Eastern Visayas (Region VIII), Philippines. Excluded from the study were individuals who did not consent to further analysis of banked samples, had insufficient plasma remaining for metabolomics analysis, had samples that were not stored at the University of California, Davis, or had acute phase protein concentrations above normal range, including plasma C-reactive protein (CRP) > 5 mg/L or plasma α-1-acid glycoprotein (AGP) > 1.0 g/L (both measured by radial immunodiffusion). For the remaining samples eligible for metabolomics analysis, participants were divided into two groups with the lowest and highest concentrations based on their plasma VA concentrations. We selected 5 participants with plasma retinol ≤ 0.8 μmol/L and 5 participants with plasma retinol >1.05 μmol/L that were our low VA (VA-, < 0.8 μmol/L) or adequate VA (VA+, > 1.05 μmol/L) status groups, respectively. It must be noted that one participant in the VA- group had a plasma retinol concentration of 0.8 μmol/L, while the remaining four participants had plasma retinol ≤ 0.7 μmol/L, the cutoff for deficiency [8]. Casual breast milk retinol per gram of fat was also measured. Plasma samples analyzed in this study were collected from the antecubital vein in 7 mL Vacutainer® tubes containing K2-EDTA (Beckton Dickinson, Franklin Lakes, NJ, USA). Blood samples were shielded from light and placed in a cooler with ice packs prior to centrifugation to obtain plasma. Separated plasma samples were aliquoted into 2 ml cryovials and stored temporarily in a refrigerator until the end of data collection that day, and then frozen at -20⁰C for ~1-4 months, until transferred to Manila on dry ice, where they were stored first at -20 ºC and then later at -80ºC. Thereafter, samples were shipped on dry ice to the University of California, Davis and stored at -80ºC until analysis. |
| Treatment Protocol Filename: | La_Frano_Treatment_Protocol_v1[23].pdf |
Sample Preparation:
| Sampleprep ID: | SP002942 |
| Sampleprep Summary: | Metabolomics assays for primary metabolomics, biogenic amines, and lipidomics were performed using protein precipitation extraction with UPLC-MS using modified previously published methods [6]. Briefly, 25 µL of plasma were added to 1.5 mL tubes before the addition of 10 µL of 1 µM internal standard solution, followed by 750 µL chilled methanol. Samples were then vortexed 30 seconds prior to being centrifuged at 15,000 x G for 10 min. The supernatant was transferred to 1.5 mL high performance liquid chromatography (HPLC) amber glass vials, dried by centrifugal vacuum evaporation, and reconstituted in 100 µL 3:1 acetonitrile: methanol solution with CUDA solution. The reconstituted solution was vortexed 30 seconds and placed on ice for 10 minutes. The solution was then centrifuged at 10,000 x G for 3 minutes after being transferred to microfilter tubes. The supernatant was then transferred to a HPLC vial to be analyzed using the UPLC-MS. |
| Sampleprep Protocol Filename: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
Combined analysis:
| Analysis ID | AN004614 | AN004615 | AN004616 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase |
| Chromatography system | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | Phenomenex Luna NH2 (150 x 2mm,3um) | Waters Atlantis HILIC (150 x 2.1 mm, 3um) | Prosphere HP C4 (150 x 3.0 mm, 3um) |
| MS Type | API | API | API |
| MS instrument type | QTRAP | QTRAP | QTRAP |
| MS instrument name | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap |
| Ion Mode | NEGATIVE | POSITIVE | POSITIVE |
| Units | Peak Area | Peak Area | Peak Area |
Chromatography:
| Chromatography ID: | CH003470 |
| Methods Filename: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Phenomenex Luna NH2 (150 x 2mm,3um) |
| Column Temperature: | 30 °C |
| Flow Gradient: | 0-10 min: 90%, 10-11 min: 5%, 11-13 min: 5%, 13-15: 90%, |
| Flow Rate: | 0.3 mL/min |
| Sample Injection: | 5µl |
| Solvent A: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide |
| Solvent B: | 75% acetonitrile/25% methanol; 10 mM ammonium hydroxide |
| Randomization Order: | Excel generated |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003471 |
| Methods Filename: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Atlantis HILIC (150 x 2.1 mm, 3um) |
| Column Temperature: | 30°C |
| Flow Gradient: | 0-1 min: 95%, 1-11 min: 95%, 11-13 min: 40%, 13-15 min: 95% |
| Flow Rate: | 0.25 mL/min |
| Sample Injection: | 5µl |
| Solvent A: | 100% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Randomization Order: | Excel generated |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003472 |
| Methods Filename: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Prosphere HP C4 (150 x 3.0 mm, 3um) |
| Column Temperature: | 30 °C |
| Flow Gradient: | 0-2 min: 20%, 2-3 min: 20%, 3-7 min: 80%, 7-10 min: 100%, 10-11 min: 100%, 11-15 min: 20% |
| Flow Rate: | 0.35 mL/min |
| Sample Injection: | 5µl |
| Solvent A: | 95% water/5% methanol; 0.1% acetic acid; 10 mM ammonium acetate |
| Solvent B: | 100% methanol; 0.1% acetic acid |
| Randomization Order: | Excel generated |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004360 |
| Analysis ID: | AN004614 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | API |
| MS Comments: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
| Ion Mode: | NEGATIVE |
| Processing Parameters File: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
| MS ID: | MS004361 |
| Analysis ID: | AN004615 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | API |
| MS Comments: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
| Ion Mode: | POSITIVE |
| Processing Parameters File: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
| MS ID: | MS004362 |
| Analysis ID: | AN004616 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | API |
| MS Comments: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
| Ion Mode: | POSITIVE |
| Processing Parameters File: | La_Frano_Lab_Methods_Doc_VA_v9[2].pdf |
