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MB Sample ID: SA338365
| Local Sample ID: | N185_LN |
| Subject ID: | SU003241 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003241 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| N185_LN | SA338365 | FL040104 | Serum | Sample source |
| N185_LN | SA338365 | FL040104 | Healthy participants | Disease |
| N185_LN | SA338365 | FL040104 | - | Causative gene |
Collection:
| Collection ID: | CO003234 |
| Collection Summary: | Patients diagnosed with IRDs, including RP, STGD, CD/CRD, and BCD, at the National Taiwan University Hospital (NTUH) between 2015 and 2020 were prospectively enrolled in this cross-sectional observational study. The study protocol adhered to the tenets of the Declaration of Helsinki and was approved by the Institutional Review Board of NTUH. Serum samples of all participants were collected within 1 to 3 p.m. without fasting status. The serum samples were stored under -80°C before analysis. |
| Sample Type: | Blood (serum) |
Treatment:
| Treatment ID: | TR003250 |
| Treatment Summary: | Not applicable |
Sample Preparation:
| Sampleprep ID: | SP003248 |
| Sampleprep Summary: | The MTBE extraction protocol, with laboratory modifications, was used to extract lipids and polar metabolites from the serum. The 10 μL internal standards (IS) mixture contains 15:0-18:1-d7-PC (2 ppm), 15:0-18:1-d7-PG (2 ppm), and L-tryptophan-(indole-d5) (10 ppm) were spiked into an aliquot of 50 μL serum. Then the sample was extracted by adding 600 μL MTBE and 150 μL MeOH and vortexed for 30 min at room temperature. Next, the sample was added with 200 μL water and centrifuged for 3 min at 13,697 g for phase separation. The upper portion containing serum lipids was transferred to another tube. The extraction was repeated by adding 100 μL water, 100 μL MeOH, and 300 μL MTBE. The sample was vortexed for an additional 10 min and centrifuged for 3 min at 13,697 g. The upper portion was mixed with the lower portion, and the combined solution was dried in a vacuum concentrator (Vacufuge plus Vacuum Concentrator, Eppendorf) for 3 h. The sample reconstitution was performed by adding 100 μL of reconstituted solution (ACN/IPA/water, v/v/v = 65/30/5). For the lower portion, 150 μL cold MeOH was added and stored under a -20°C environment for 2 h, followed by 10 min of 21,401 g centrifugation for protein precipitation. Next, the supernatant was dried using a vacuum concentrator overnight and then reconstituted by adding 100 μL reconstituted solution (ACN/water, v/v = 50/50). The protein precipitation was repeated by mixing 60 μL reconstituted sample with 120 μL cold ACN and then putting the mixtures in a -20°C freezer for an hour. After a 15 min centrifugation at 21,401 g under 4°C, super supernatants (120 μL) were collected and stored under -80°C before further analysis. |
Combined analysis:
| Analysis ID | AN005119 | AN005120 | AN005121 | AN005122 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH003873 |
| Chromatography Summary: | Chromatography methods for lipid extract, positive-ion mode. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 50℃ |
| Flow Gradient: | 0–1 min, 15% B; 1–15 min, 15–70% B; 15-16 min, 70–99% B; 16–18.5 min, 99% B; 18.5–19 min, 99–15% B; and 19-–21 min, 15% B |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | Acetonitrile/water (4/6); 0.1% formic acid |
| Solvent B: | Isopropyl alcohol/acetonitrile (9/1); 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003874 |
| Chromatography Summary: | Chromatography methods for lipid extract, negative-ion mode. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 50℃ |
| Flow Gradient: | 0–0.5 min, 15% B; 0.5–4 min, 15–70% B; 4–15 min, 70–99% B; 15–16.5 min, 99% B; 16.15–17 min, 99–15% B; and 17–19 min, 15% B |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | Acetonitrile/water (4/6); 5 mM ammonium acetate |
| Solvent B: | Isopropyl alcohol/acetonitrile (9/1); 5 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003875 |
| Chromatography Summary: | Chromatography methods for metabolite extract, positive-ion mode. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 40℃ |
| Flow Gradient: | 0–1 min, 90% B; 1–9 min, 90-40% B; 9–11.5 min, 40% B; 11.5–12 min, 40–90% B; and 12–14 min, 90% B |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% Water; 0.1% formic acid |
| Solvent B: | 100% Acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003876 |
| Chromatography Summary: | Chromatography methods for metabolite extract, negative-ion mode. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 40℃ |
| Flow Gradient: | 0–1 min, 90% B; 1–9 min, 90-40% B; 9–11.5 min, 40% B; 11.5–12 min, 40–90% B; and 12–14 min, 90% B |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% Water; 5 mM ammonium acetate |
| Solvent B: | 100% Acetonitrile; 5 mM ammonium acetate |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004855 |
| Analysis ID: | AN005119 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS data were processed using Thermo Scientific Compound Discoverer v3.2 software. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 280℃ |
| Ion Source Temperature: | 180℃ |
| Ion Spray Voltage: | 3.5 kV |
| MS ID: | MS004856 |
| Analysis ID: | AN005120 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS data were processed using Thermo Scientific Compound Discoverer v3.2 software. |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 280℃ |
| Ion Source Temperature: | 180℃ |
| Ion Spray Voltage: | -3.5 kV |
| MS ID: | MS004857 |
| Analysis ID: | AN005121 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS data were processed using Thermo Scientific Compound Discoverer v3.2 software. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 280℃ |
| Ion Source Temperature: | 180℃ |
| Ion Spray Voltage: | 3.5 kV |
| MS ID: | MS004858 |
| Analysis ID: | AN005122 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS data were processed using Thermo Scientific Compound Discoverer v3.2 software. |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 280℃ |
| Ion Source Temperature: | 180℃ |
| Ion Spray Voltage: | -3.5 kV |
