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MB Sample ID: SA232353
| Local Sample ID: | plasma # 31 |
| Subject ID: | SU002424 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002424 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| plasma # 31 | SA232353 | FL029147 | WM3311 LCT | Sample description |
| plasma # 31 | SA232353 | FL029147 | plasma | Tissue |
Collection:
| Collection ID: | CO002417 |
| Collection Summary: | Human melanoma xenografts were established in mice using A375 and WM47 (BRAF mutant), WM3311 (BRAF/NRAS wild-type) and WM3000 (NRAS mutant) cells. Blood was taken by cardiac puncture, collected in heparin-coated tubes and centrifuged for 3 min at 2000 g. Plasma samples were stored at -80 °C until analysis. Tumors were harvested and snap frozen in liquid nitrogen and stored at -80°C for metabolomics. |
| Sample Type: | Blood (plasma) and tumor tissue |
Treatment:
| Treatment ID: | TR002436 |
| Treatment Summary: | Human melanoma xenografts were established in mice using A375 and WM47 (BRAF mutant), WM3311 (BRAF/NRAS wild-type) and WM3000 (NRAS mutant) cells. Once the tumor volume reached 100 mm3, mice were equally assigned to control diet (CTRL) and two ketogenic diet (KDs) differing in their fat composition (LCT: long-chain triglyceride-based KD and LCT-MCT: long-chain triglyceride-based KD supplemented with C8 and C10 medium-chain triglycerides, ratio of fat to the sum of carbohydrate and protein of 8:1). Both KDs were administered ad libitum as monotherapy. |
Sample Preparation:
| Sampleprep ID: | SP002430 |
| Sampleprep Summary: | To capture a broad spectrum of metabolites, we used the MxP® Quant 500 kit combined with the in-house acylcarnitine (AC) assay (biocrates life sciences ag). Samples were prepared the same way for both assays. Therefore, 50-80 mg of tumor tissues were transferred to 0.5 ml Precellys® vials followed by the addition of 85:15 ethanol:0.01 M phosphate as a lysis buffer with a volume [µl] of 3 times the tissue weight [mg]. Tissue homogenization was carried out at 4 °C and 5800 rpm using a Precellys® 24 homogenizer coupled to a Cryolys® cooling unit. The homogenates were centrifuged at 10,000 g for 2 min at 2-4 °C. Supernatants were collected and stored at -80 °C until analysis. Plasma samples as well as tissue homogenate supernatant were thawed on ice, then vortexed before use. |
Combined analysis:
| Analysis ID | AN003815 | AN003816 | AN003817 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | Reversed phase | None (Direct infusion) | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity | Thermo Dionex Ultimate 3000 |
| Column | MxP Quant 500 Kit System | MxP Quant 500 Kit System | Biocrates Acylcarnitine |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | Waters TQ-S MS | Waters TQ-S MS | Thermo TQS Vantage |
| Ion Mode | POSITIVE | UNSPECIFIED | POSITIVE |
| Units | uM | uM | uM |
Chromatography:
| Chromatography ID: | CH002822 |
| Instrument Name: | Waters Acquity |
| Column Name: | MxP Quant 500 Kit System |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002823 |
| Instrument Name: | Waters Acquity |
| Column Name: | MxP Quant 500 Kit System |
| Chromatography Type: | None (Direct infusion) |
| Chromatography ID: | CH002824 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Biocrates Acylcarnitine |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003557 |
| Analysis ID: | AN003815 |
| Instrument Name: | Waters TQ-S MS |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | MS acquisition data were obtained using MRM transition (Q1 and Q3 pair) in positive ion mode. Raw data of the MxP® Quant 500 assay were exported and quantified using MetIDQTM software (Biocrates Life Sciences). Downstream analysis was performed using MetaboAnalyst 5.0. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003558 |
| Analysis ID: | AN003816 |
| Instrument Name: | Waters TQ-S MS |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | MS acquisition data were obtained using MRM transition (Q1 and Q3 pair) in positive and negative ion mode. Raw data of the MxP® Quant 500 assay were exported and quantified using MetIDQTM software (Biocrates Life Sciences). Downstream analysis was performed using MetaboAnalyst 5.0. |
| Ion Mode: | UNSPECIFIED |
| MS ID: | MS003559 |
| Analysis ID: | AN003817 |
| Instrument Name: | Thermo TQS Vantage |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | MS acquisition data were obtained using MRM transition (Q1 and Q3 pair) in positive ion mode. Raw data files of the AC assay were generated by using XcaliburTM software (Thermo Fisher) and exported to MetIDQTM for further analysis, including peak integration, retention time correction, area calculation, calibration curve preparation and concentration calculation. Downstream analysis was performed using MetaboAnalyst 5.0. |
| Ion Mode: | POSITIVE |
