Summary of Study ST001887

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	ST001887
Study Title	Untargeted lipidomics of hypertrophic cardiomyopathy (part II)
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:	SU001965
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

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

mb_sample_id	local_sample_id	Group
SA175291	D1331	Donor
SA175292	D1234	Donor
SA175293	D2552	Donor
SA175294	D2554	Donor
SA175295	D2507	Donor
SA175296	D2540	Donor
SA175297	M2803	Hypertophic cardiomyopathy
SA175298	M2800	Hypertophic cardiomyopathy
SA175299	M2856	Hypertophic cardiomyopathy
SA175300	M2799	Hypertophic cardiomyopathy
SA175301	M2939	Hypertophic cardiomyopathy
SA175302	M2860	Hypertophic cardiomyopathy
SA175303	M1455	Hypertophic cardiomyopathy
SA175304	M467	Hypertophic cardiomyopathy
SA175305	M433	Hypertophic cardiomyopathy
SA175306	M1385	Hypertophic cardiomyopathy
SA175307	M2622	Hypertophic cardiomyopathy
SA175308	M2673	Hypertophic cardiomyopathy
SA175309	M2692	Hypertophic cardiomyopathy

Showing results 1 to 19 of 19

Showing results 1 to 19 of 19

Collection:

Collection ID:	CO001958
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:	TR001977
Treatment Summary:	N/A

Sample Preparation:

Sampleprep ID:	SP001971
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:

SP001971

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	AN003055	AN003056
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000 RS	Thermo Dionex Ultimate 3000 RS
Column	Thermo Accucore (150 x 2.1mm,2.6um)	Thermo Accucore (150 x 2.1mm,2.6um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	MS count (log2)	MS count (log2)

Chromatography:

Chromatography ID:	CH002262
Chromatography Summary:	Lipid extracts were also analyzed using an Ultimate 3000 RSLC system coupled with a Q Exactive mass spectrometer (Thermo Scientific, Waltham, MA) as previously described6. Each sample was run twice in positive and negative ionization modes. Lipids were separated using an Accucore C18 column 2.1 x 150 mm, 2.6 μm (Thermo Scientific) and mobile phase solvents consisted in 10 mM ammonium acetate and 0.1% formic acid in 60/40 acetonitrile/water (A) and 10 mM ammonium acetate and 0.1% formic acid in 90/10 isopropanol/acetonitrile (B). The Q Exactive was equipped with a HESI-II prob
Instrument Name:	Thermo Dionex Ultimate 3000 RS
Column Name:	Thermo Accucore (150 x 2.1mm,2.6um)
Solvent A:	60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium acetate
Solvent B:	90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium acetate
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002842
Analysis ID:	AN003055
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	LC-MS peak extraction, alignment, quantification and annotation was performed using LipidSearch software version 4.2 (Thermo Scientific). Only lipids present in >2/3 of the samples were kept for further analysis. Median normalization (excluding TAG and DAG) 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. Lipids were identified by matching the precursor ion mass to a database and the experimental MS/MS spectra to a spectral library containing theoretical fragmentation spectra. The identity of cardiolipins, detected as [M-H]-, was manually validated by investigating individual MS/MS spectra. Lipid abundances were reported as spectral counts.
Ion Mode:	POSITIVE

MS ID:	MS002843
Analysis ID:	AN003056
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	LC-MS peak extraction, alignment, quantification and annotation was performed using LipidSearch software version 4.2 (Thermo Scientific). Only lipids present in >2/3 of the samples were kept for further analysis. Median normalization (excluding TAG and DAG) 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. Lipids were identified by matching the precursor ion mass to a database and the experimental MS/MS spectra to a spectral library containing theoretical fragmentation spectra. The identity of cardiolipins, detected as [M-H]-, was manually validated by investigating individual MS/MS spectra. Lipid abundances were reported as spectral counts.
Ion Mode:	NEGATIVE