Summary of Study ST002817

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 PR001748. The data can be accessed directly via it's Project DOI: 10.21228/M8RQ7M 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002817
Study TitleInvestigation of metabolism in hypertrophic cardiomyopathy - Lipidomics
Study SummaryWe propose the use of targeted metabolomics to define the metabolic and molecular pathways altered in 2 mouse models (R92W-TnT and R403Q-MHC) of hypertrophic cardiomyopathy (HCM) that span the spectrum of human disease (heart failure and sudden death), with the goal of identifying treatment targets. Parallel targeted metabolomics studies will be performed in heart tissue and plasma at rest and following inotrope stimulation. Since energy compromise is expected to be most marked when the heart is subject to increased workload, as is the case during high-intensity exercise or inotropic stimulation, we propose metabolomics studies in heart tissue and plasma, at rest and following inotrope stimulation. We anticipate that the results of these studies will allow us to move forward with further investigations into specific metabolites of interest as biomarkers, to be tested in HCM patients in future studies.
Institute
University of California, San Francisco
DepartmentHypertrophic Cardiomyopathy Center of Excellence
LaboratoryUCSF Smith Cardiovascular Research Building
Last NameAbraham
First NameMaria Roselle
Address555 Mission Bay Boulevard South, San Francisco, CA 94158
EmailRoselle.Abraham@ucsf.edu
Phone415-502-3911
Submit Date2023-07-27
Num Groups2 groups of 2 (i.e., mutant vs control of two mouse models of HCM (R402Q-MyHC, R92W-TnT)
Total Subjects32
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2023-09-06
Release Version1
Maria Roselle Abraham Maria Roselle Abraham
https://dx.doi.org/10.21228/M8RQ7M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001748
Project DOI:doi: 10.21228/M8RQ7M
Project Title:Investigation of metabolism in hypertrophic cardiomyopathy
Project Summary:We propose the use of targeted metabolomics to define the metabolic and molecular pathways altered in 2 mouse models (R92W-TnT and R403Q-MHC) of hypertrophic cardiomyopathy (HCM) that span the spectrum of human disease (heart failure and sudden death), with the goal of identifying treatment targets. Parallel targeted metabolomics studies will be performed in heart tissue and plasma at rest and following inotrope stimulation. Since energy compromise is expected to be most marked when the heart is subject to increased workload, as is the case during high-intensity exercise or inotropic stimulation, we propose metabolomics studies in heart tissue and plasma, at rest and following inotrope stimulation. We anticipate that the results of these studies will allow us to move forward with further investigations into specific metabolites of interest as biomarkers, to be tested in HCM patients in future studies.
Institute:University of California, San Francisco
Department:Hypertrophic Cardiomyopathy Center of Excellence
Laboratory:UCSF Smith Cardiovascular Research Building
Last Name:Abraham
First Name:Maria Roselle
Address:555 Mission Bay Boulevard South, San Francisco, CA 94158
Email:Roselle.Abraham@ucsf.edu
Phone:415-502-3911
Contributors:Arpana Vaniya (avaniya@ucdavis.edu), Anja Karlstaedt (Anja.Karlstaedt@cshs.org)

Subject:

Subject ID:SU002926
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 Treatment
SA302586M503Control MHC
SA302587M499Control MHC
SA302588M447Control MHC
SA302589M487Control MHC
SA302590M492Control MHC
SA302591M438Control MHC
SA302592M440Control MHC
SA302593M485Control MHC
SA302594T545Control TNT
SA302595T547Control TNT
SA302596T544Control TNT
SA302597T520Control TNT
SA302598T515Control TNT
SA302599T524Control TNT
SA302600T518Control TNT
SA302601T522Control TNT
SA302610MtdBlank004Method Blank
SA302611MtdBlank002Method Blank
SA302612MtdBlank005Method Blank
SA302613MtdBlank003Method Blank
SA302614MtdBlank007Method Blank
SA302615MtdBlank001Method Blank
SA302616MtdBlank008Method Blank
SA302617MtdBlank006Method Blank
SA302602M540MHC
SA302603M498MHC
SA302604M486MHC
SA302605M439MHC
SA302606M483MHC
SA302607M500MHC
SA302608M441MHC
SA302609M504MHC
SA302618Pool001Pool QC
SA302619Pool002Pool QC
SA302620Pool004Pool QC
SA302621Pool003Pool QC
SA302622Pool005Pool QC
SA302623Pool006Pool QC
SA302624Pool008Pool QC
SA302625Pool007Pool QC
SA302626Biorec001QC
SA302627Biorec002QC
SA302628Biorec006QC
SA302629Biorec005QC
SA302630Biorec007QC
SA302631Biorec008QC
SA302632Biorec003QC
SA302633Biorec004QC
SA302634T527TNT
SA302635T521TNT
SA302636T519TNT
SA302637T523TNT
SA302638T525TNT
SA302639T542TNT
SA302640T540TNT
SA302641T546TNT
Showing results 1 to 56 of 56

Collection:

Collection ID:CO002919
Collection Summary:Excision while the heart still beating and flash freeze within 15 seconds of excision
Sample Type:Heart

Treatment:

Treatment ID:TR002935
Treatment Summary:Saline IP and heparine SC injection in control & mutant group. After 10 minutes of saline injection we performed cervical dislocation, whole heart excision and flash freeze within 15 seconds of excision.

Sample Preparation:

Sampleprep ID:SP002932
Sampleprep Summary:2 mg of lyophilized tissue extracted with 225 uL MeOH + 188 uL H2O + 750 uL MTBE. 350 uL of the organic layer was dried and resuspended 90:10 MeOH + Toluene with internal standards.

Combined analysis:

Analysis ID AN004584 AN004585 AN004586
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase
Chromatography system Agilent 1290 Agilent 1290 Waters Acquity
Column Waters ACQUITY UPLC CSH C18 (100 x 1mm,1.7um) Waters ACQUITY UPLC CSH C18 (100 x 1mm,1.7um) Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI ESI
MS instrument type QTOF QTOF Orbitrap
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE
Units peak heights peak heights raw area counts rescaled to set the median equal to 1

Chromatography:

Chromatography ID:CH003445
Chromatography Summary:-
Instrument Name:Agilent 1290
Column Name:Waters ACQUITY UPLC CSH C18 (100 x 1mm,1.7um)
Column Temperature:65C
Flow Gradient:0 min 15% (B), 0–2 min 30% (B), 2–2.5 min 48% (B), 2.5–11 min 82% (B), 11–11.5 min 99% (B), 11.5– 12 min 99% (B), 12–12.1 min 15% (B), 12.1–15 min 15% (B)
Flow Rate:0.6 mL/min
Solvent A:60:40 v/v acetonitrile:water + 10 mM ammonium formate + 0.1% formic acid
Solvent B:90:10 v/v isopropanol:acetonitrile + 10 mM ammonium formate + 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH003446
Chromatography Summary:Low pH polar (LC/MS Pos early)
Instrument Name:Waters Acquity
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:-
Flow Gradient:-
Flow Rate:-
Solvent A:-
Solvent B:-
Chromatography Type:Reversed phase

MS:

MS ID:MS004330
Analysis ID:AN004584
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The quadrupole/time-of-flight (QTOF) mass spectrometers are operated with electrospray ionization (ESI) performing full scan in the mass range m/z 65–1700 in positive (Agilent 6530, equipped with a JetStreamSource) and negative (Agilent 6550, equipped with a dual JetStream Source) modes producing both unique and complementary spectra. Instrument parameters are as follows (positive mode) Gas Temp 325°C, Gas Flow 8 l/min, Nebulizer 35 psig, Sheath Gas 350°C, Sheath Gas Flow 11, Capillary Voltage 3500 V, Nozzle Voltage 1000V, Fragmentor 120V, Skimmer 65V. Data (both profile and centroid) are collected at a rate of 2 scans per second. In negative ion mode, Gas Temp 200°C, Gas Flow 14 l/min, Fragmentor 175V, with the other parameters identical to positive ion mode. For the 6530 QTOF, a reference solution generating ions of 121.050 and 922.007 m/z in positive mode and 119.036 and 966.0007 m/z in negative mode, and these are used for continuous mass correction. For the 6550, the reference solution is introduced via a dual spray ESI, with the same ions and continuous mass correction
Ion Mode:POSITIVE
  
MS ID:MS004331
Analysis ID:AN004585
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The quadrupole/time-of-flight (QTOF) mass spectrometers are operated with electrospray ionization (ESI) performing full scan in the mass range m/z 65–1700 in positive (Agilent 6530, equipped with a JetStreamSource) and negative (Agilent 6550, equipped with a dual JetStream Source) modes producing both unique and complementary spectra. Instrument parameters are as follows (positive mode) Gas Temp 325°C, Gas Flow 8 l/min, Nebulizer 35 psig, Sheath Gas 350°C, Sheath Gas Flow 11, Capillary Voltage 3500 V, Nozzle Voltage 1000V, Fragmentor 120V, Skimmer 65V. Data (both profile and centroid) are collected at a rate of 2 scans per second. In negative ion mode, Gas Temp 200°C, Gas Flow 14 l/min, Fragmentor 175V, with the other parameters identical to positive ion mode. For the 6530 QTOF, a reference solution generating ions of 121.050 and 922.007 m/z in positive mode and 119.036 and 966.0007 m/z in negative mode, and these are used for continuous mass correction. For the 6550, the reference solution is introduced via a dual spray ESI, with the same ions and continuous mass correction
Ion Mode:NEGATIVE
  
MS ID:MS004332
Analysis ID:AN004586
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Pos early)
Ion Mode:POSITIVE
  logo