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MB Sample ID: SA254700
| Local Sample ID: | 20210804_14 |
| Subject ID: | SU002630 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002630 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 20210804_14 | SA254700 | FL032634 | ASS1KO;mASS1 | Sample type |
Collection:
| Collection ID: | CO002623 |
| Collection Summary: | Tumors were rapidly dissected after euthanizing animals. Tumors were weighed and rinsed in blood bank saline solution (150 mM NaCl) and blotted on filter paper (VWR, Radnor, PA, 28298–020). The process of dissection and tumor preparation took < 3min. Tumors were cut in half and put onto 20µm nylon mesh filters (Spectrum Labs, Waltham, MA, 148134) on top of 50 mL conical tubes, and centrifuged for 10min. at 4°C at 400xg. IF was then collected, snap-frozen in liquid nitrogen and stored at -80°C until further analysis. |
| Sample Type: | Interstitial Fluid |
Treatment:
| Treatment ID: | TR002642 |
| Treatment Summary: | Orthotopic tumors were implanted in C57BL6J mice at 8-12 weeks of age. 4 weeks after induction interstitial fluid and tumors were collected. |
Sample Preparation:
| Sampleprep ID: | SP002636 |
| Sampleprep Summary: | polar metabolites were extracted from 5µL IF samples using 45µL 75:25:0.1 HPLC grade acetonitrile:methanol:formic acid extraction mix into which a mixture of isotopically labeled amino acids of known concentrations (Cambridge Isotope Laboratories, MSK-A2-1.2) was added. Samples were vortexed for 10 min, and centrifuged at maximum speed for 10 min. 30 μL of each extract was removed and dried under nitrogen gas and stored −80°C. |
Combined analysis:
| Analysis ID | AN004164 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | Waters XBridge Amide (100 x 4.6mm, 3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | Peak area (m/z) |
Chromatography:
| Chromatography ID: | CH003083 |
| Chromatography Summary: | HPLC |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters XBridge Amide (100 x 4.6mm, 3.5um) |
| Column Temperature: | 25 |
| Flow Gradient: | 0 min, 15% A; 2.5 min, 64% A; 12.4 min, 40% A; 12.5 min, 30% A; 12.5-14 min, 30% A; 14-21 min, 15% A |
| Flow Rate: | 150 μL/min |
| Solvent A: | 95% water/5% acetonitrile; 10 mM ammonium hydroxide; 10 mM ammonium acetate, pH = 9.0 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003911 |
| Analysis ID: | AN004164 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | In positive/negative polarity switching mode, an m/z scan range from 60 to 900 was chosen and MS1 data was collected at a resolution of 70,000. The automatic gain control (AGC) target was set at 1 × 106 and the maximum injection time was 200 ms. The targeted ions were subsequently fragmented, using the higher energy collisional dissociation (HCD) cell set to 30% normalized collision energy in MS2 at a resolution power of 17,500. Besides matching m/z, target metabolites are identified by matching either retention time with analytical standards and/or MS2 fragmentation pattern. Data acquisition and analysis were carried out by Xcalibur 4.1 software and Tracefinder 4.1 software, respectively (both from Thermo Fisher Scientific). |
| Ion Mode: | UNSPECIFIED |
