Summary of Study ST001886

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 PR001189. The data can be accessed directly via it's Project DOI: 10.21228/M8140K 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 ID	ST001886
Study Title	Untargeted metabolomics of hypertrophic cardiomyopathy (part I)
Study Summary	Hypertrophic cardiomyopathy (HCM) is a complex disease partly explained by the effects of individual gene variants on sarcomeric protein biomechanics. At the cellular level, HCM mutations most commonly enhance force production, leading to higher energy demands. Despite significant advances in elucidating sarcomeric structure-function relationships, there is still much to be learned about the mechanisms that link altered cardiac energetics to HCM phenotypes. In this work, we test the hypothesis that changes in cardiac energetics represent a common pathophysiologic pathway in HCM.
Institute	Stanford University
Last Name	Contrepois
First Name	Kevin
Address	300 Pasteur Dr
Email	kcontrep@stanford.edu
Phone	6506664538
Submit Date	2021-07-13
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-07-13
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001189
Project DOI:	doi: 10.21228/M8140K
Project Title:	Multi-omics study of hypertrophic cardiomyopathy
Project Summary:	Multi-omics study of human heart tissues in the context of hypertrophic cardiomyopathy
Institute:	Stanford University
Last Name:	Contrepois
First Name:	Kevin
Address:	300 Pasteur Dr
Email:	kcontrep@stanford.edu
Phone:	6506664538

Subject:

Subject ID:	SU001964
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Species Group:	Mammals

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Group
SA175269	D2540	Donor
SA175270	D2554	Donor
SA175271	D2507	Donor
SA175272	D2552	Donor
SA175273	D1331	Donor
SA175274	D1234	Donor
SA175275	M2799	Hypertophic cardiomyopathy
SA175276	M2800	Hypertophic cardiomyopathy
SA175277	M2803	Hypertophic cardiomyopathy
SA175278	M2860	Hypertophic cardiomyopathy
SA175279	M2692	Hypertophic cardiomyopathy
SA175280	M2939	Hypertophic cardiomyopathy
SA175281	M2856	Hypertophic cardiomyopathy
SA175282	M1455	Hypertophic cardiomyopathy
SA175283	M467	Hypertophic cardiomyopathy
SA175284	M433	Hypertophic cardiomyopathy
SA175285	M2673	Hypertophic cardiomyopathy
SA175286	M1385	Hypertophic cardiomyopathy
SA175287	M2622	Hypertophic cardiomyopathy
SA175288	A1067	Hypertrophy control
SA175289	A2971	Hypertrophy control
SA175290	MS270	Mitral stenosis

Showing results 1 to 22 of 22

Showing results 1 to 22 of 22

Collection:

Collection ID:	CO001957
Collection Summary:	Cardiac tissue was excised and a mid-myocardial portion was used immediately for studies of mitochondrial respiration, or fixed in 4% paraformaldehyde (PFA) for paraffin embedding or in 4% PFA and 2% glutaraldehyde for TEM analysis. The remaining tissue was flash frozen in liquid nitrogen for all other assays.
Sample Type:	Heart

Treatment:

Treatment ID:	TR001976
Treatment Summary:	N/A

Sample Preparation:

Sampleprep ID:	SP001970
Sampleprep Summary:	Sample Preparation. Roughly 30 mg of frozen heart tissue were homogenized in 500 µl ice-cold methanol by bead beating (MP bioscience cat# 6913-100, Solon, OH) at 4°C (2 x 45 s). Metabolites and complex lipids were extracted using a biphasic separation with cold methyl tert-butyl ether (MTBE), methanol and water. Briefly, 1 ml of ice-cold MTBE was added to 300 μl of the homogenate spiked-in with 40 µl deuterated lipid internal standards (Sciex, cat#: 5040156, lot#: LPISTDKIT-101). The samples were then sonicated (3 x 30 s) and agitated at 4°C for 30 min. After addition of 250 μl of ice-cold water, the samples were vortexed for 1 min and centrifuged at 14,000 g for 5 min at 20°C. The upper organic phase contains the lipids, the lower aqueous phase contains the metabolites and the proteins are precipitated at the bottom of the tube. For quality controls, 3 reference plasma samples (40 µl plasma) and 1 preparation blank were processed in parallel. 1) Metabolites: Proteins were further precipitated by adding 700 μl of 33/33/33 acetone/acetonitrile/methanol spiked-in with 15 labeled metabolite internal standards to 300 μl of the aqueous phase and 200 μl of the lipid phase and incubating the samples overnight at -20°C. After centrifugation at 17,000 g for 10 min at 4°C, the metabolic extracts were dried down to completion and resuspended in 100 μl 50/50 methanol/water. 2) Complex lipids: 700 µl of the organic phase was dried down under a stream of nitrogen and resolubilized in 200 μl of methanol for storage at -20°C until analysis. The day of the analysis, samples were dried down, resuspended in 300 μl of 10 mM ammonium acetate in 90/10 methanol/toluene and centrifuged at 16,000 g for 5 min at 24°C.

Sampleprep ID:

SP001970

Sampleprep Summary:

Sample Preparation. Roughly 30 mg of frozen heart tissue were homogenized in 500 µl ice-cold methanol by bead beating (MP bioscience cat# 6913-100, Solon, OH) at 4°C (2 x 45 s). Metabolites and complex lipids were extracted using a biphasic separation with cold methyl tert-butyl ether (MTBE), methanol and water. Briefly, 1 ml of ice-cold MTBE was added to 300 μl of the homogenate spiked-in with 40 µl deuterated lipid internal standards (Sciex, cat#: 5040156, lot#: LPISTDKIT-101). The samples were then sonicated (3 x 30 s) and agitated at 4°C for 30 min. After addition of 250 μl of ice-cold water, the samples were vortexed for 1 min and centrifuged at 14,000 g for 5 min at 20°C. The upper organic phase contains the lipids, the lower aqueous phase contains the metabolites and the proteins are precipitated at the bottom of the tube. For quality controls, 3 reference plasma samples (40 µl plasma) and 1 preparation blank were processed in parallel. 1) Metabolites: Proteins were further precipitated by adding 700 μl of 33/33/33 acetone/acetonitrile/methanol spiked-in with 15 labeled metabolite internal standards to 300 μl of the aqueous phase and 200 μl of the lipid phase and incubating the samples overnight at -20°C. After centrifugation at 17,000 g for 10 min at 4°C, the metabolic extracts were dried down to completion and resuspended in 100 μl 50/50 methanol/water. 2) Complex lipids: 700 µl of the organic phase was dried down under a stream of nitrogen and resolubilized in 200 μl of methanol for storage at -20°C until analysis. The day of the analysis, samples were dried down, resuspended in 300 μl of 10 mM ammonium acetate in 90/10 methanol/toluene and centrifuged at 16,000 g for 5 min at 24°C.

Combined analysis:

Analysis ID	AN003051	AN003052	AN003053	AN003054
Analysis type	MS	MS	MS	MS
Chromatography type	HILIC	HILIC	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000 RS	Thermo Dionex Ultimate 3000 RS	Thermo Dionex Ultimate 3000 RS	Thermo Dionex Ultimate 3000 RS
Column	SeQuant ZIC-HILIC (100 x 2.1mm,3.5um)	SeQuant ZIC-HILIC (100 x 2.1mm,3.5um)	Agilent Zorbax SBaq (50 x 2.1mm,1.7um)	Agilent Zorbax SBaq (50 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 Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE
Units	MS count (log2)	MS count (log2)	MS count (log2)	MS count (log2)

Chromatography:

Chromatography ID:	CH002260
Chromatography Summary:	HILIC experiments were performed using a ZIC-HILIC column 2.1 x 100 mm, 3.5 μm, 200Å (Merck Millipore, Darmstadt, Germany) and mobile phase solvents consisting of 10 mM ammonium acetate in 50/50 acetonitrile/water (A) and 10 mM ammonium acetate in 95/5 acetonitrile/water (B).
Instrument Name:	Thermo Dionex Ultimate 3000 RS
Column Name:	SeQuant ZIC-HILIC (100 x 2.1mm,3.5um)
Solvent A:	50% acetonitrile/50% water; 10 mM ammonium acetate
Solvent B:	95% acetonitrile/5% water; 10 mM ammonium acetate
Chromatography Type:	HILIC

Chromatography ID:	CH002261
Chromatography Summary:	RPLC experiments were performed using a Zorbax SBaq column 2.1 x 50 mm, 1.7 μm, 100Å (Agilent Technologies, Palo Alto, CA) and mobile phase solvents consisting of 0.06% acetic acid in water (A) and 0.06% acetic acid in methanol (B).
Instrument Name:	Thermo Dionex Ultimate 3000 RS
Column Name:	Agilent Zorbax SBaq (50 x 2.1mm,1.7um)
Solvent A:	100% water; 0.06% acetic acid
Solvent B:	100% methanol; 0.06% acetic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002838
Analysis ID:	AN003051
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and those that didn’t show sufficient linearity upon dilution in QC samples (r<0.6) were discarded. Only metabolic features present in >2/3 of the samples were kept for further analysis. Median normalization was applied to correct for differential starting material quantity. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Data from each mode were merged and metabolites of interest were formally identified by matching fragmentation spectra and retention time to analytical-grade standards when possible or matching experimental MS/MS to fragmentation spectra in publicly available databases.
Ion Mode:	POSITIVE

MS ID:	MS002839
Analysis ID:	AN003052
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and those that didn’t show sufficient linearity upon dilution in QC samples (r<0.6) were discarded. Only metabolic features present in >2/3 of the samples were kept for further analysis. Median normalization was applied to correct for differential starting material quantity. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Data from each mode were merged and metabolites of interest were formally identified by matching fragmentation spectra and retention time to analytical-grade standards when possible or matching experimental MS/MS to fragmentation spectra in publicly available databases.
Ion Mode:	NEGATIVE

MS ID:	MS002840
Analysis ID:	AN003053
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and those that didn’t show sufficient linearity upon dilution in QC samples (r<0.6) were discarded. Only metabolic features present in >2/3 of the samples were kept for further analysis. Median normalization was applied to correct for differential starting material quantity. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Data from each mode were merged and metabolites of interest were formally identified by matching fragmentation spectra and retention time to analytical-grade standards when possible or matching experimental MS/MS to fragmentation spectra in publicly available databases.
Ion Mode:	POSITIVE

MS ID:	MS002841
Analysis ID:	AN003054
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and those that didn’t show sufficient linearity upon dilution in QC samples (r<0.6) were discarded. Only metabolic features present in >2/3 of the samples were kept for further analysis. Median normalization was applied to correct for differential starting material quantity. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Data from each mode were merged and metabolites of interest were formally identified by matching fragmentation spectra and retention time to analytical-grade standards when possible or matching experimental MS/MS to fragmentation spectra in publicly available databases.
Ion Mode:	NEGATIVE