Summary of Study ST003197

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 PR001988. The data can be accessed directly via it's Project DOI: 10.21228/M8RJ07 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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST003197
Study TitleUQ/RQ panel on wildtype mouse tissue
Study SummaryThe extraction of nonpolar metabolites from the tissues of wildtype mice for analysis by LCMS to measure levels of Ubiquinone and Rhodoquinone.
Institute
UMass Chan Medical School
DepartmentProgram in Molecular Medicine
LaboratorySpinelli Lab
Last NameJerome
First NameMadison
Address55 N Lake Ave, Worcester, MA 01655
Emailmadison.jerome@umassmed.edu
Phone(508) 856-8989 ext. 68148
Submit Date2024-04-19
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-02-04
Release Version1
Madison Jerome Madison Jerome
https://dx.doi.org/10.21228/M8RJ07
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001988
Project DOI:doi: 10.21228/M8RJ07
Project Title:Rhodoquinone is an Electron Carrier in the Mammalian Electron Transport Chain
Project Summary:Ubiquinone (UQ), the only known electron carrier in the mammalian electron transport chain (ETC), delivers electrons to both oxygen (O2) and fumarate as terminal electron acceptors. As fumarate has a lower reduction potential than UQ, fumarate reduction is only thermodynamically favorable when ubiquinol, the reduced form of UQ, accumulates. Paradoxically, some tissues reduce fumarate without ubiquinol buildup, suggesting another mechanism enables fumarate reduction in mammals. Here, we identify rhodoquinone (RQ), a novel mammalian electron carrier that directs electrons to fumarate, instead of O2, as the favored terminal electron acceptor. RQ, which is undetectable in cultured mammalian cells, is enriched in tissues that catalyze fumarate reduction. RQ and UQ-directed ETC circuits support distinct programs of mitochondrial function. Through expression of a bacterial enzyme that converts UQ into RQ and development a novel RQ analog, we demonstrate that reprogramming the mammalian ETC from the UQ to RQ circuit renders cells highly resistant to hypoxia exposure. Thus, we establish RQ as a fundamental component of the mammalian ETC and unveil reprogramming the ETC to the RQ-circuit as a tractable strategy to treat hypoxia-related diseases.
Institute:UMass Chan Medical School
Department:Program in Molecular Medicine
Laboratory:Spinelli Lab
Last Name:UMass Chan
First Name:Spinelli Lab
Address:55 Lake Avenue North, Worcester, Massachusetts, 01605, USA
Email:spinellilab@gmail.com
Phone:(508) 856-8989 ext. 68148

Subject:

Subject ID:SU003316
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Sample source Sample type
SA347971MITO_B04BRAIN Mitochondria
SA347972MITO_B05BRAIN Mitochondria
SA347973MITO_B07BRAIN Mitochondria
SA347974MITO_B03BRAIN Mitochondria
SA347975MITO_B06BRAIN Mitochondria
SA347976MITO_B01BRAIN Mitochondria
SA347977WholeTissue_B01BRAIN Whole Tissue
SA347978WholeTissue_B07BRAIN Whole Tissue
SA347979WholeTissue_B03BRAIN Whole Tissue
SA347980WholeTissue_B04BRAIN Whole Tissue
SA347981WholeTissue_B06BRAIN Whole Tissue
SA347982WholeTissue_B05BRAIN Whole Tissue
SA347983CoQ9_01CoQ9 0.001µM Standard CoQ9 Standard
SA347984CoQ9_02CoQ9 0.01µM Standard CoQ9 Standard
SA347985CoQ9_03CoQ9 0.1µM Standard CoQ9 Standard
SA347986CoQ9_04CoQ9 0.25µM Standard CoQ9 Standard
SA347987CoQ9_05CoQ9 0.5µM Standard CoQ9 Standard
SA347988CoQ9_08CoQ9 10µM Standard CoQ9 Standard
SA347989CoQ9_06CoQ9 1µM Standard CoQ9 Standard
SA347990CoQ9_07CoQ9 5µM Standard CoQ9 Standard
SA347991MITO_H05HEART Mitochondria
SA347992MITO_H06HEART Mitochondria
SA347993MITO_H04HEART Mitochondria
SA347994MITO_H01HEART Mitochondria
SA347995MITO_H02HEART Mitochondria
SA347996MITO_H03HEART Mitochondria
SA347997WholeTissue_H06HEART Whole Tissue
SA347998WholeTissue_H05HEART Whole Tissue
SA347999WholeTissue_H01HEART Whole Tissue
SA348000WholeTissue_H03HEART Whole Tissue
SA348001WholeTissue_H04HEART Whole Tissue
SA348002WholeTissue_H07HEART Whole Tissue
SA348003MITO_IWAT05INGUINAL WHITE ADIPOSE TISSUE Mitochondria
SA348004MITO_IWAT06INGUINAL WHITE ADIPOSE TISSUE Mitochondria
SA348005MITO_IWAT07INGUINAL WHITE ADIPOSE TISSUE Mitochondria
SA348006MITO_IWAT04INGUINAL WHITE ADIPOSE TISSUE Mitochondria
SA348007MITO_IWAT03INGUINAL WHITE ADIPOSE TISSUE Mitochondria
SA348008MITO_IWAT01INGUINAL WHITE ADIPOSE TISSUE Mitochondria
SA348009WholeTissue_IWAT07INGUINAL WHITE ADIPOSE TISSUE Whole Tissue
SA348010WholeTissue_IWAT06INGUINAL WHITE ADIPOSE TISSUE Whole Tissue
SA348011WholeTissue_IWAT01INGUINAL WHITE ADIPOSE TISSUE Whole Tissue
SA348012WholeTissue_IWAT05INGUINAL WHITE ADIPOSE TISSUE Whole Tissue
SA348013WholeTissue_IWAT04INGUINAL WHITE ADIPOSE TISSUE Whole Tissue
SA348014WholeTissue_IWAT03INGUINAL WHITE ADIPOSE TISSUE Whole Tissue
SA348015MITO_KID04KIDNEY Mitochondria
SA348016MITO_KID03KIDNEY Mitochondria
SA348017MITO_KID05KIDNEY Mitochondria
SA348018MITO_KID06KIDNEY Mitochondria
SA348019MITO_KID07KIDNEY Mitochondria
SA348020MITO_KID01KIDNEY Mitochondria
SA348021WholeTissue_KID07KIDNEY Whole Tissue
SA348022WholeTissue_KID06KIDNEY Whole Tissue
SA348023WholeTissue_KID05KIDNEY Whole Tissue
SA348024WholeTissue_KID01KIDNEY Whole Tissue
SA348025WholeTissue_KID03KIDNEY Whole Tissue
SA348026WholeTissue_KID04KIDNEY Whole Tissue
SA348027MITO_LIV03LIVER Mitochondria
SA348028MITO_LIV04LIVER Mitochondria
SA348029MITO_LIV01LIVER Mitochondria
SA348030MITO_LIV05LIVER Mitochondria
SA348031MITO_LIV06LIVER Mitochondria
SA348032MITO_LIV07LIVER Mitochondria
SA348033WholeTissue_LIV05LIVER Whole Tissue
SA348034WholeTissue_LIV06LIVER Whole Tissue
SA348035WholeTissue_LIV03LIVER Whole Tissue
SA348036WholeTissue_LIV01LIVER Whole Tissue
SA348037WholeTissue_LIV04LIVER Whole Tissue
SA348038WholeTissue_LIV07LIVER Whole Tissue
SA348039MITO_LUNG01LUNG Mitochondria
SA348040MITO_LUNG05LUNG Mitochondria
SA348041MITO_LUNG07LUNG Mitochondria
SA348042MITO_LUNG06LUNG Mitochondria
SA348043MITO_LUNG04LUNG Mitochondria
SA348044MITO_LUNG03LUNG Mitochondria
SA348045WholeTissue_LUNG07LUNG Whole Tissue
SA348046WholeTissue_LUNG05LUNG Whole Tissue
SA348047WholeTissue_LUNG01LUNG Whole Tissue
SA348048WholeTissue_LUNG03LUNG Whole Tissue
SA348049WholeTissue_LUNG04LUNG Whole Tissue
SA348050WholeTissue_LUNG06LUNG Whole Tissue
SA348051MITO_M03MUSCLE Mitochondria
SA348052MITO_M04MUSCLE Mitochondria
SA348053MITO_M01MUSCLE Mitochondria
SA348054MITO_M07MUSCLE Mitochondria
SA348055MITO_M06MUSCLE Mitochondria
SA348056MITO_M05MUSCLE Mitochondria
SA348057WholeTissue_M01MUSCLE Whole Tissue
SA348058WholeTissue_M03MUSCLE Whole Tissue
SA348059WholeTissue_M07MUSCLE Whole Tissue
SA348060WholeTissue_M04MUSCLE Whole Tissue
SA348061WholeTissue_M05MUSCLE Whole Tissue
SA348062WholeTissue_M06MUSCLE Whole Tissue
SA348063MITO_P05PANCREAS Mitochondria
SA348064MITO_P06PANCREAS Mitochondria
SA348065MITO_P01PANCREAS Mitochondria
SA348066MITO_P07PANCREAS Mitochondria
SA348067MITO_P03PANCREAS Mitochondria
SA348068MITO_P04PANCREAS Mitochondria
SA348069WholeTissue_P04PANCREAS Whole Tissue
SA348070WholeTissue_P07PANCREAS Whole Tissue
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 104

Collection:

Collection ID:CO003309
Collection Summary:Tissues were harvested, flash frozen in liquid nitrogen, and stored at -80°C until samples were ready for processing.
Sample Type:Kidney, Brain, Pancreas, Heart, Lung, Muscle, inguinal white adipose tissue & Liver

Treatment:

Treatment ID:TR003325
Treatment Summary:Wildtype untreated

Sample Preparation:

Sampleprep ID:SP003323
Sampleprep Summary:---UQRQ isolation from tissues: Tissues were flash frozen in liquid nitrogen and powderized using a mortar and pestle. Approximately 10 mg of tissue powder was transferred into an Eppendorf tube. The tissue powder was re-suspended in 500 µL of 99.9% LCMS-grade methanol (Fisher) 0.1% HCl and then vortexed for 15 minutes at 4°C. 500 µL LCMS-grade hexane (Honeywell) was added to the lysate and again vortexed for 15 minutes at 4°C. Samples were then centrifuged at 16,000 x g for 10 minutes at 4°C with the top (hexane) layer containing UQ and RQ, the middle layer containing the acidified methanol, and the bottom layer containing the protein. The top layer was transferred into a new Eppendorf tube, dried down in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap-105 Cold Trap (Labconco), and stored at -80°C until they were re-suspended for LC-MS analysis. The acidified methanol layer was discarded, and the bottom protein layer was saved for protein quantification. The protein layer from the metabolite isolation was re-suspended in 1 mL of RIPA buffer (150 mM NaCl, 50 mM Tris HCl pH 7.5, 0.1% SDS, 1% Triton-X 100 (Sigma), 0.5% deoxycholate (Sigma), cOmplete EDTA-free protease inhibitor (Sigma)). The samples were vortexed for 10 minutes at 4°C and then centrifuged at 16,000 x g for 10 minutes at 4°C. Protein concentrations for each sample were calculated using the Pierce BCA Protein Assay Kit (Life Technologies). The protein concentrations were used to calculate the re-suspension volume to normalize all samples for LC-MS analysis to equal (20 µg/µL ) concentration. ---Isolation of mitochondria from tissues: Purified mitochondria pellets were subsequently vortexed in 500 µL of 99.9% LCMS-grade methanol (Fisher) 0.1% HCl for 10 minutes at 4°C. 500 µL of 100% LCMS-grade hexane (Honeywell) was added to each tube and vortexed for an additional 10 minutes at 4°C. Samples were then centrifuged for 10 minutes at 21,300 x g at 4°C. The top (hexane) layer of the sample (containing UQ and RQ) was transferred to a new labeled 1.5 mL Eppendorf tube and dried in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap-105 Cold Trap (Labconco). Samples were stored in -80°C freezer prior to resuspension and running on LC-MS. The bottom layer was discarded and the pellet was saved for protein quantification. Protein was isolated as described above. Protein concentrations were calculated using the Pierce BCA Protein Assay Kit (Life Technologies). The protein concentrations were used to calculate the re-suspension volume to normalize all samples for LC-MS analysis to equal (20 µg/uL) concentration. ---Isolation of UQ/RQ from purified mitochondria: Purified mitochondria pellets were subsequently vortexed in 500 µL of 99.9% LCMS-grade methanol (Fisher) 0.1% HCl for 10 minutes at 4°C. 500 µL of 100% LCMS-grade hexane (Honeywell) was added to each tube and vortexed for an additional 10 minutes at 4°C. Samples were then centrifuged for 10 minutes at 21,300 x g at 4°C. The top (hexane) layer of the sample (containing UQ and RQ) was transferred to a new labeled 1.5 mL Eppendorf tube and dried in a Refrigerated CentriVap Benchtop Vacuum Concentrator connected to a CentriVap-105 Cold Trap (Labconco). Samples were stored in -80°C freezer prior to resuspension and running on LC-MS. The bottom layer was discarded and the pellet was saved for protein quantification. Protein was isolated as described above. Protein concentrations were calculated using the Pierce BCA Protein Assay Kit (Life Technologies). The protein concentrations were used to calculate the re-suspension volume to normalize all samples for LC-MS analysis to equal (20 µg/uL) concentration.

Combined analysis:

Analysis ID AN005247
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Phenomenex Luna PFP(2) (100 x 2mm,3µm)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH003972
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Luna PFP(2) (100 x 2mm,3µm)
Column Temperature:25
Flow Gradient:0 - 3 min, 30% A; 3 - 3.25 min, 30% - 2% A; 3.25 - 5min, 2% A; 5 - 6min, 2% - 1% A; 6 - 8.75min, 1% A; 8.75 - 9min, 1% - 30% A; 9 - 10min, 30% A
Flow Rate:0.5ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS004980
Analysis ID:AN005247
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The mass spectrometer was operated in full scan, positive-ion mode, with the spray voltage set to 3.0 kV, the heated capillary at 275°C, and the HESI probe at 350°C. The sheath gas flow was 40 units, the auxiliary gas flow was 15 units, and the sweep gas flow was 1 unit. MS data was collected in a range of m/z = 200 –1000. The resolution set at 17,500, the AGC target at 3x106, and the maximum injection time at 250 msec. Data acquired by Thermo Fisher's Xcalibur software and analyzed by their Tracefinder software. The data reported includes the different adducts and reduced forms of the metabolites to show presence or lack thereof.
Ion Mode:POSITIVE
  logo