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MB Sample ID: SA081276
Local Sample ID: | 1 |
Subject ID: | SU001237 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Gender: | Female |
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Subject:
Subject ID: | SU001237 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Gender: | Female |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
1 | SA081276 | FL012392 | pre | Group |
Collection:
Collection ID: | CO001231 |
Collection Summary: | Blood samples were collected via retro-orbital bleeding after anesthesia, from 22 TKO-Pre mice (average age, 2.0 months; age range, 1.3–3.1), 10 TKO-ET mice (4.8 months: 2.5–5.9), 16 TKO-AT mice (6.4 months: 4.3–10.1), 19 TKO-ctrl mice (3.0 months: 3.0–8.2), and 17 UT mice (5.4 months: 3.7–6.8). Blood samples were centrifuged at 14,000 rpm for 5 minutes at room temperature, and serum was collected and stored at -80 °C until UPLC-MS analysis. |
Sample Type: | Blood (serum) |
Treatment:
Treatment ID: | TR001252 |
Treatment Summary: | Triple-mutant (TKO) mice (p53 LSL-R172H/+ Dicer1 flox/flox Pten flox/flox Amhr2 cre/+) were generated by mating p53 LSL-R172H/+ Dicer1 flox/flox Pten flox/flox female with Dicer1 flox/flox Pten flox/flox Amhr2 cre/+ male mice. Serum samples were collected from TKO mice at different stages of tumor progression: from premalignant stage to early stage to advanced stage. Precursor lesions are fallopian tubes at premalignant stage, when no tumors are yet present. TKO mice with precursor (i.e. premalignant stage) lesions in the fallopian tubes are referred to as “TKO-Pre”; TKO-ET (early tumor) are TKO mice with early-stage tumors in the fallopian tube without evidence of metastasis; TKO-AT (advanced-stage tumor) are TKO mice with ovarian and peritoneal metastases accompanied by ascites; and TKO-ctrl are control mice (p53 LSL-R172H/+ Dicer1 flox/flox Pten flox/flox), which have the same genetic background as TKO mice but develop no tumors. All TKO mice developed high-grade serous carcinoma (HGSC, i.e. high-grade serous ovarian cancer). |
Sample Preparation:
Sampleprep ID: | SP001245 |
Sampleprep Summary: | Serum samples were thawed on ice and subject to two different sample preparation protocols to profile either non-polar or polar sub-metabolomes. Reverse phase (RP) and hydrophilic interaction liquid chromatography (HILIC) UPLC-MS analysis were used for these different polarity metabolite fractions to obtain complementary information. Methanol (for polar) or iso-propanol (for non-polar) was added to a 50 μL serum sample in a 3:1 ratio to precipitate proteins. Samples were vortex mixed for 10 s and centrifuged at 13,000 rpm for 7 min. Then, 150 μL supernatant was frozen at -80 °C for UPLC-MS analysis. A sample blank was prepared with 50 μL of LC-MS grade water, and a pooled quality control (QC) sample was created by mixing 10 μL aliquot of each serum sample. Both the sample blank and the pooled sample were processed with the same procedure as the murine serum samples. Solvent blanks and sample blanks were analyzed together with murine serum samples. |
Combined analysis:
Analysis ID | AN001937 | AN001938 | AN001939 | AN001940 |
---|---|---|---|---|
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 BEH C18 (50 x 2.1mm,1.7um) | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) | Waters Acquity BEH HILIC (150 x 2.1mm,1.7um) | Waters Acquity BEH HILIC (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 HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
Units | chromatographic peak area | chromatographic peak area | chromatographic peak area | chromatographic peak area |
Chromatography:
Chromatography ID: | CH001406 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
Column Temperature: | 55 |
Sample Injection: | 5μL |
Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate |
Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH001407 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Waters Acquity BEH HILIC (150 x 2.1mm,1.7um) |
Column Temperature: | 55 |
Sample Injection: | 2μL |
Solvent A: | 95% water/5% acetonitrile; 0.05% ammonium hydroxide; 10 mM ammonium acetate |
Solvent B: | 100% acetonitrile; 0.05% ammonium hydroxide |
Chromatography Type: | HILIC |
MS:
MS ID: | MS001793 |
Analysis ID: | AN001937 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Samples were analyzed in positive and negative ion modes for both RP and HILIC chromatography. Spectral features were extracted from the raw data using Compound Discoverer v2.1 software. |
Ion Mode: | POSITIVE |
Capillary Temperature: | 275 °C |
Spray Voltage: | 3.0 kV |
MS ID: | MS001794 |
Analysis ID: | AN001938 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Samples were analyzed in positive and negative ion modes for both RP and HILIC chromatography. Spectral features were extracted from the raw data using Compound Discoverer v2.1 software. |
Ion Mode: | NEGATIVE |
Capillary Temperature: | 275 °C |
Spray Voltage: | -2.8 kV |
MS ID: | MS001795 |
Analysis ID: | AN001939 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Samples were analyzed in positive and negative ion modes for both RP and HILIC chromatography. Spectral features were extracted from the raw data using Compound Discoverer v2.1 software. |
Ion Mode: | POSITIVE |
Capillary Temperature: | 275 °C |
Spray Voltage: | 3.0 kV |
MS ID: | MS001796 |
Analysis ID: | AN001940 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Samples were analyzed in positive and negative ion modes for both RP and HILIC chromatography. Spectral features were extracted from the raw data using Compound Discoverer v2.1 software. |
Ion Mode: | NEGATIVE |
Capillary Temperature: | 275 °C |
Spray Voltage: | -2.8 kV |