Summary of Study ST002137

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 PR001353. The data can be accessed directly via it's Project DOI: 10.21228/M8TQ43 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 IDST002137
Study TitleTargeted Microchip Capillary Electrophoresis-Orbitrap Mass Spectrometry Metabolomics to Monitor Ovarian Cancer Progression. (Ovarian cancer mouse data)
Study SummaryThe lack of effective screening strategies for high-grade serous carcinoma (HGSC), a subtype of ovarian cancer (OC) responsible for 80% of OC related deaths, emphasizes the need for new diagnostic markers and a better understanding of disease pathogenesis. Capillary electrophoresis (CE) coupled with high-resolution mass spectrometry (HRMS) offers high selectivity and sensitivity, thereby increasing metabolite coverage and consequently enhancing biomarker discovery. Recent advances in CE-MS include small, chip-based CE systems coupled with nanoelectrospray ionization (nanoESI) to provide rapid, high-resolution analysis of biological specimens. Here, we describe the development of a targeted microchip (µ) CE-HRMS method to analyze 40 target metabolites in serum samples from a triple-mutant (TKO) mouse model of HGSC, with an acquisition time of only 3 min. Extracted ion electropherograms showed sharp, highly resolved peak shapes, even for structural isomers such as leucine and isoleucine. All analytes maintained good linearity with an average R2 of 0.994, while detection limits were in the nM range. Thirty metabolites were detected in mice serum, with recoveries ranging from 78 to 120 %, indicating minimal ionization suppression and good accuracy. We applied the µCE-HRMS method to sequentially-collected serum samples from TKO and TKO-control mice. Time-resolved analysis revealed characteristic temporal trends for amino acids, nucleosides, and amino acids derivatives associated with HGSC progression. Comparison of the µCE-HRMS dataset with non-targeted ultra-high performance liquid chromatography (UHPLC) – MS results revealed identical temporal trends for the 5 metabolites detected on both platforms, indicating the µCE-HRMS method performed satisfactorily in terms of capturing metabolic reprogramming due to HGSC progression, while reducing the total analysis time 3-fold.
Institute
Georgia Institute of Technology
Last NameSah
First NameSamyukta
Address901 Atlantic Dr NW, Atlanta, GA, 30332, USA
Emailssah9@gatech.edu
Phone5746780124
Submit Date2022-04-11
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-05-02
Release Version1
Samyukta Sah Samyukta Sah
https://dx.doi.org/10.21228/M8TQ43
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001353
Project DOI:doi: 10.21228/M8TQ43
Project Title:Targeted Microchip Capillary Electrophoresis-Orbitrap Mass Spectrometry Metabolomics to Monitor Ovarian Cancer Progression.
Project Summary:The lack of effective screening strategies for high-grade serous carcinoma (HGSC), a subtype of ovarian cancer (OC) responsible for 80% of OC related deaths, emphasizes the need for new diagnostic markers and a better understanding of disease pathogenesis. Capillary electrophoresis (CE) coupled with high-resolution mass spectrometry (HRMS) offers high selectivity and sensitivity, thereby increasing metabolite coverage and consequently enhancing biomarker discovery. Recent advances in CE-MS include small, chip-based CE systems coupled with nanoelectrospray ionization (nanoESI) to provide rapid, high-resolution analysis of biological specimens. Here, we describe the development of a targeted microchip (µ) CE-HRMS method to analyze 40 target metabolites in serum samples from a triple-mutant (TKO) mouse model of HGSC, with an acquisition time of only 3 min. Extracted ion electropherograms showed sharp, highly resolved peak shapes, even for structural isomers such as leucine and isoleucine. All analytes maintained good linearity with an average R2 of 0.994, while detection limits were in the nM range. Thirty metabolites were detected in mice serum, with recoveries ranging from 78 to 120 %, indicating minimal ionization suppression and good accuracy. We applied the µCE-HRMS method to sequentially-collected serum samples from TKO and TKO-control mice. Time-resolved analysis revealed characteristic temporal trends for amino acids, nucleosides, and amino acids derivatives associated with HGSC progression. Comparison of the µCE-HRMS dataset with non-targeted ultra-high performance liquid chromatography (UHPLC) – MS results revealed identical temporal trends for the 5 metabolites detected on both platforms, indicating the µCE-HRMS method performed satisfactorily in terms of capturing metabolic reprogramming due to HGSC progression, while reducing the total analysis time 3-fold.
Institute:Georgia Institute of Technology
Last Name:Sah
First Name:Samyukta
Address:901 Atlantic Dr NW, Atlanta, GA, 30332, USA
Email:ssah9@gatech.edu
Phone:5746780124

Subject:

Subject ID:SU002222
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id pheotype
SA205252C10_3Control
SA205253C10_2Control
SA205254C10_1Control
SA205255C10_4Control
SA205256C10_5Control
SA205257C10_7Control
SA205258C10_6Control
SA205259C8_14Control
SA205260C8_12Control
SA205261C8_8Control
SA205262C8_7Control
SA205263C8_6Control
SA205264C8_9Control
SA205265C8_10Control
SA205266C10_8Control
SA205267C8_11Control
SA205268C8_13Control
SA205269C10_10Control
SA205270C13_9Control
SA205271C13_8Control
SA205272C13_7Control
SA205273C13_10Control
SA205274C13_11Control
SA205275C13_13Control
SA205276C13_12Control
SA205277C13_6Control
SA205278C13_5Control
SA205279C10_12Control
SA205280C10_11Control
SA205281C8_5Control
SA205282C13_1Control
SA205283C13_2Control
SA205284C13_4Control
SA205285C13_3Control
SA205286C10_9Control
SA205287C8_4Control
SA205288C8_2Control
SA205289C8_1Control
SA205290C8_3Control
SA205291T11_3TKO
SA205292T11_2TKO
SA205293T11_1TKO
SA205294T11_4TKO
SA205295T11_6TKO
SA205296T11_7TKO
SA205297T13_9TKO
SA205298T11_5TKO
SA205299T13_7TKO
SA205300T13_3TKO
SA205301T13_2TKO
SA205302T13_4TKO
SA205303T13_5TKO
SA205304T11_8TKO
SA205305T13_6TKO
SA205306T13_8TKO
SA205307T11_11TKO
SA205308T15_7TKO
SA205309T15_6TKO
SA205310T15_8TKO
SA205311T15_9TKO
SA205312T15_11TKO
SA205313T15_10TKO
SA205314T15_5TKO
SA205315T15_3TKO
SA205316T11_12TKO
SA205317T13_1TKO
SA205318T11_13TKO
SA205319T11_14TKO
SA205320T15_1TKO
SA205321T11_15TKO
SA205322T11_10TKO
Showing results 1 to 71 of 71

Collection:

Collection ID:CO002215
Collection Summary:TKO p53LSL R172H/+ Dicer1flox/flox Ptenflox/flox Amhr2cre/+ mice were generated by mating p53LSL-R172H/+Dicer1flox/floxPtenflox/flox female mice with Dicer1flox/floxPtenflox/floxAmhr2cre/+ male mice. For TKO controls, p53LSL-R172H/+Dicer1flox/floxPtenflox/flox were generated. TKO control mice carry the same genetic makeup as TKO mice but do not develop HGSC. A sequential serum collection protocol was conducted to collect samples from TKO and TKO controls every two weeks starting at 8 weeks of age until a humane end point for sacrifice or development of ascites. TKO mice were sacrificed at Indiana University School of Medicine in accordance with animal protocol (21124) approved by the IACUC.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR002234
Treatment Summary:TKO p53LSL R172H/+ Dicer1flox/flox Ptenflox/flox Amhr2cre/+ mice were generated by mating p53LSL-R172H/+Dicer1flox/floxPtenflox/flox female mice with Dicer1flox/floxPtenflox/floxAmhr2cre/+ male mice. For TKO controls, p53LSL-R172H/+Dicer1flox/floxPtenflox/flox were generated. TKO control mice carry the same genetic makeup as TKO mice but do not develop HGSC. A sequential serum collection protocol was conducted to collect samples from TKO and TKO controls every two weeks starting at 8 weeks of age until a humane end point for sacrifice or development of ascites. TKO mice were sacrificed at Indiana University School of Medicine in accordance with animal protocol (21124) approved by the IACUC.

Sample Preparation:

Sampleprep ID:SP002228
Sampleprep Summary:An extraction solvent consisting of a mixture of isotopically labeled internal standards including 808 µM 13C6 arginine and 212 µM 13C methionine D3 was added to methanol in a 1:60 ratio and stored at 4 °C until further use. Serum samples were thawed on ice, followed by protein precipitation in a 10 µl serum aliquot with extraction solvent in a 1:3 ratio. Samples were vortexed for 30 s and centrifuged at 13,000 rpm for 7 min. To enhance CE peak shape, the resulting supernatant was diluted in a 1:4 ratio with the sample diluent containing 133 mM ammonium acetate, 0.1% formic acid and 1 µM 13C phenylalanine.

Combined analysis:

Analysis ID AN003498
Analysis type MS
Chromatography type CE
Chromatography system ZipChip (908 Devices)
Column HS chip
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap
Ion Mode POSITIVE
Units Micromolars

Chromatography:

Chromatography ID:CH002584
Instrument Name:ZipChip (908 Devices)
Column Name:HS chip
Chromatography Type:CE

MS:

MS ID:MS003258
Analysis ID:AN003498
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:µCE-HRMS analyses were performed using the microchip ZipChip® capillary electrophoresis system (classic interface, 908 Devices, Boston MA), coupled to a high-resolution accurate mass Q Exactive plus mass spectrometer (Thermo Fisher Scientific, MA). µCE-HRMS separations used ZipChip® HS chips (10 cm channel). All experiments were performed in positive ionization mode in the 50-500 m/z range at a mass resolution setting of 17,500. The capillary temperature was set to 200 °C and the sheath gas flow rate was 2 psi. The automatic gain control (AGC) target value was set to 3E6 and the maximum injection time was 20 ms. Data were acquired using Xcalibur 3.0 (Thermo Scientific) and were imported to Skyline software14 for peak picking and integration. The peak picking procedure used the analyte accurate m/z and migration time. Peak areas obtained from Skyline were exported as spreadsheets for further analysis. Quantitation was performed with the analyte peak areas relative to the peak area of one of the three isotopically labeled internal standards (13C6 arginine, 13C methionine D3 and 13C phenylalanine) chosen based on migration time similarities
Ion Mode:POSITIVE
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