Return to study ST001670 main page
MB Sample ID: SA153403
| Local Sample ID: | CC 02030 metabo reg control 003 |
| Subject ID: | SU001747 |
| Subject Type: | Fish |
| Subject Species: | Danio rerio |
| Taxonomy ID: | 7955 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001747 |
| Subject Type: | Fish |
| Subject Species: | Danio rerio |
| Taxonomy ID: | 7955 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| CC 02030 metabo reg control 003 | SA153403 | FL017920 | control | Treatment |
Collection:
| Collection ID: | CO001740 |
| Collection Summary: | Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Please refer to the publication for more details. |
| Sample Type: | Larvae |
Treatment:
| Treatment ID: | TR001760 |
| Treatment Summary: | Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Please refer to the publication for more details. |
Sample Preparation:
| Sampleprep ID: | SP001753 |
| Sampleprep Summary: | Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Metabolites were extracted from 5 pooled larvae, and 6 replicates were used per condition. Metabolites were extracted as described previously36. Some of the replicates were used to optimize the analysis of polar metabolites and folate derivatives using Vanquish UHPLC (Thermo Fisher Scientific). Please refer to the publication for more details. |
Combined analysis:
| Analysis ID | AN002725 | AN002726 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Vanquish UHPLC (Thermo Fisher Scientific). | Thermo Vanquish UHPLC |
| Column | Waters Xbridge amide HILIC (100 x 2.1mm,3.5um) | Luna C18 LC (150 x 4.6 mm,3um) |
| MS Type | ESI | ESI |
| MS instrument type | Ion trap | Ion trap |
| MS instrument name | Thermo Orbitrap Exploris 480 | Thermo Orbitrap Exploris 480 |
| Ion Mode | UNSPECIFIED | UNSPECIFIED |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH002011 |
| Chromatography Summary: | For this polar metabolite analysis, a hydrophilic interaction chromatography method (HILIC) with an Xbridge amide column (100 x 2.1 mm i.d., 3.5 µm; Waters) was used for compound separation at 25 °C. Mobile phase A: water with 5 mM ammonium acetate (pH 6.8), and mobile phase B: 100 % acetonitrile. Linear gradient was: 0 min, 85% B; 1.5 min, 85% B; 5.5 min, 35% B; 6.9 min, 35% B; 10.5 min, 35% B; 10.6 min, 10% B; 12.5 min, 10% B; 13.5 min, 85% B; 17.9 min, 85% B; 18 min, 85% B; 20 min, 85% B. The flow rate was: 0-5.5 min, 0.11 ml/min; 6.9-10.5 min, 0.13 ml/min; 10.6-17.9 min, 0.25 ml/min; 18-20 min, 0.11 ml/min. |
| Instrument Name: | Vanquish UHPLC (Thermo Fisher Scientific). |
| Column Name: | Waters Xbridge amide HILIC (100 x 2.1mm,3.5um) |
| Column Temperature: | 25 |
| Flow Gradient: | 0 min, 85% B; 1.5 min, 85% B; 5.5 min, 35% B; 6.9 min, 35% B; 10.5 min, 35% B; 10.6 min, 10% B; 12.5 min, 10% B; 13.5 min, 85% B; 17.9 min, 85% B; 18 min, 85% B; 20 min, 85% B. |
| Flow Rate: | 0-5.5 min, 0.11 ml/min; 6.9-10.5 min, 0.13 ml/min; 10.6-17.9 min, 0.25 ml/min; 18-20 min, 0.11 ml/min |
| Solvent A: | 100% water; 5 mM ammonium acetate, pH 6.8 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH002012 |
| Chromatography Summary: | The analysis of folic acid and its derivatives was performed using Luna column (100 x 3 mm i.d., 3 µm, C18(2), 100 Å, Phenomenex) at 25 °C. Mobile phase A: water with 0.1% formic acid, and mobile phase B: 100 % methanol. Linear gradient was: 0 min, 2% B; 1.5 min, 2% B; 3.0 min, 15% B; 5.5 min, 95% B; 14.5 min, 95% B; 15.0 min, 2% B; 22.0 min, 2% B. The flow rate was 0.150 ml/min. |
| Chromatography Comments: | Luna® 3 µm C18(2) 100 Å, LC Column 150 x 4.6 mm, Ea |
| Instrument Name: | Thermo Vanquish UHPLC |
| Column Name: | Luna C18 LC (150 x 4.6 mm,3um) |
| Column Temperature: | 25 |
| Flow Gradient: | 0 min, 2% B; 1.5 min, 2% B; 3.0 min, 15% B; 5.5 min, 95% B; 14.5 min, 95% B; 15.0 min, 2% B; 22.0 min, 2% B. |
| Flow Rate: | 0.150 ml/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002522 |
| Analysis ID: | AN002725 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | Xcalibur 4.4 from Thermo Scientific for data acquisition and we use Sieve 2.2 for chromatographic alignment and peak integration.To analyze polar metabolites, the mass spectrometer was equipped with a HESI probe and operated in the positive/negative switching mode. The relevant parameters were as listed: vaporizer temperature, 350 °C; ion transfer tube temperature, 300 °C; sheath gas, 35; auxiliary gas, 7; sweep gas, 1; spray voltage, 3.5 kV for positive mode and 2.5 kV for negative mode; RF-lens (%), 30. The resolution was set at 60,000 (at m/z 200). Automatic maximum injection time (max IT) and automated gain control (AGC) were used. |
| Ion Mode: | UNSPECIFIED |
| MS ID: | MS002523 |
| Analysis ID: | AN002726 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | Xcalibur 4.4 from Thermo Scientific for data acquisition and we use Sieve 2.2 for chromatographic alignment and peak integration.To measure folate derivatives, Orbitrap Exploris 480 was operated in SIM mode (selected ion monitoring) targeting the following ions: folic acid (442.1470), 5-methyltetrahydrofolate (460.1939), and folinic acid (474.1732). |
| Ion Mode: | UNSPECIFIED |
