Summary of Study ST001172

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000784. The data can be accessed directly via it's Project DOI: 10.21228/M8BH6F This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001172
Study TitleDeep Metabolomics of a High-Grade Serous Ovarian Cancer Triple Knockout Mouse Model.
Study TypeUntargeted metabolomics
Study SummaryMetabolic alternations were investigated by applying Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) to serum samples collected from triple knockout (TKO) mice at pre-malignant, early, and advanced stages of HGSC. Samples were analyzed with control mice, which have the same genetic background as TKO mice but develop no tumors. To enhance the selectivity for HGSC-specific metabolite markers, a tumor control group was also included. These were uterine tumor (UT) mice that developed uterine tumors, but no HGSC. All samples were analyzed using reverse phase (RP) and hydrophilic interaction liquid chromatography (HILIC) UPLC-MS analysis in positive and negative ion modes.
Institute
Georgia Institute of Technology
DepartmentChemistry
LaboratoryFernández
Last NameHuang
First NameDanning
Address901 Atlantic Dr NE
Emaildhuang74@gatech.edu
Phone4045127523
Submit Date2019-04-16
Num Groups5
Total Subjects84
Num Females84
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-10-11
Release Version1
Danning Huang Danning Huang
https://dx.doi.org/10.21228/M8BH6F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000784
Project DOI:doi: 10.21228/M8BH6F
Project Title:Deep Metabolomics of a High-Grade Serous Ovarian Cancer Triple Knockout Mouse Model.
Project Type:Untargeted metabolomics
Project Summary:High-grade serous carcinoma (HGSC) is the most common and deadliest ovarian cancer (OC) type, accounting for 70–80% of OC deaths. This high mortality is largely due to late diagnosis. Early detection is thus crucial to reduce mortality. Yet tumor pathogenesis of HGSC remains poorly understood, making early detection difficult. Faithfully and reliably representing the clinical nature of human HGSC, a recently-developed triple knockout (TKO) mouse model offers a unique opportunity to examine the entire disease spectrum of HGSC. Deep metabolomics study was performed to serum samples collected from these mice to understand the metabolic alternations associated with HGSC development and progression, and provide guidance toward early detection.
Institute:Georgia Institute of Technology
Department:Chemistry
Laboratory:Fernández
Last Name:Huang
First Name:Danning
Address:901 Atlantic Dr NE, Atlanta, GA, 30332, USA
Email:dhuang74@gatech.edu
Phone:404-512-7523

Subject:

Subject ID:SU001237
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Gender:Female

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA08123938ctrl
SA08124028ctrl
SA08124129ctrl
SA08124230ctrl
SA08124327ctrl
SA08124426ctrl
SA08124523ctrl
SA08124624ctrl
SA08124725ctrl
SA08124841ctrl
SA08124931ctrl
SA08125037ctrl
SA08125139ctrl
SA08125240ctrl
SA08125332ctrl
SA08125436ctrl
SA08125533ctrl
SA08125634ctrl
SA08125735ctrl
SA08119646ET
SA08119745ET
SA08119844ET
SA08119947ET
SA08120049ET
SA08120151ET
SA08120250ET
SA08120342ET
SA08120448ET
SA08120543ET
SA08120656LT
SA08120755LT
SA08120857LT
SA08120959LT
SA08121060LT
SA08121154LT
SA08121253LT
SA08121365LT
SA08121467LT
SA08121566LT
SA08121652LT
SA08121761LT
SA08121858LT
SA08121962LT
SA08122063LT
SA08122164LT
SA0812582pre
SA0812596pre
SA08126018pre
SA08126119pre
SA08126220pre
SA08126321pre
SA08126417pre
SA08126516pre
SA08126613pre
SA08126714pre
SA08126815pre
SA08126922pre
SA08127011pre
SA08127112pre
SA0812725pre
SA0812734pre
SA0812747pre
SA0812758pre
SA0812761pre
SA08127710pre
SA0812789pre
SA0812793pre
SA08122269UT
SA08122368UT
SA08122470UT
SA08122571UT
SA08122673UT
SA08122774UT
SA08122875UT
SA08122984UT
SA08123082UT
SA08123177UT
SA08123272UT
SA08123376UT
SA08123478UT
SA08123579UT
SA08123681UT
SA08123780UT
SA08123883UT
Showing results 1 to 84 of 84

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
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