Summary of Study ST002717

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 PR001684. The data can be accessed directly via it's Project DOI: 10.21228/M81H71 This work is supported by NIH grant, U2C- DK119886.

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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 IDST002717
Study TitleVentricle-specific myocardial protein and metabolite characterisation in healthy humans, with differential regulation in end-stage cardiomyopathies (Part 2)
Study SummaryThe left and right ventricles of the human heart are functionally and developmentally distinct such that genetic or acquired insults can cause dysfunction in one or both ventricles resulting in heart failure. First, we performed unbiased quantitative mass spectrometry on the myocardium of 25-27 pre-mortem cryopreserved non-diseased human hearts to compare the metabolome and proteome between the normal left and right ventricles. Constituents of gluconeogenesis, glycolysis, lipogenesis, lipolysis, fatty acid catabolism, the citrate cycle and oxidative phosphorylation were down-regulated in the left ventricle, while glycogenesis, pyruvate and ketone metabolism were up-regulated. Inter-ventricular significance of these metabolic pathways was then found to be diminished within end-stage dilated cardiomyopathy and ischaemic cardiomyopathy (n = 30-33), while heart failure-associated pathways were increased in the left ventricle relative to the right within ischaemic cardiomyopathy, such as fluid sheer-stress, increased glutamine to glutamate ratio, and down-regulation of contractile proteins indicating a left ventricular pathological bias.
Institute
University of Sydney
Last NameHunter
First NameBenjamin
AddressJohn Hopkins Dr, Camperdown, NSW, 2006, Australia
Emailbenjamin.hunter@sydney.edu.au
Phone+61422525639
Submit Date2023-05-25
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-06-27
Release Version1
Benjamin Hunter Benjamin Hunter
https://dx.doi.org/10.21228/M81H71
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001684
Project DOI:doi: 10.21228/M81H71
Project Title:Ventricle-specific myocardial protein and metabolite characterisation in healthy humans, with differential regulation in end-stage cardiomyopathies
Project Summary:The left and right ventricles of the human heart are functionally and developmentally distinct such that genetic or acquired insults can cause dysfunction in one or both ventricles resulting in heart failure. First, we performed unbiased quantitative mass spectrometry on the myocardium of 25-27 pre-mortem cryopreserved non-diseased human hearts to compare the metabolome and proteome between the normal left and right ventricles. Constituents of gluconeogenesis, glycolysis, lipogenesis, lipolysis, fatty acid catabolism, the citrate cycle and oxidative phosphorylation were down-regulated in the left ventricle, while glycogenesis, pyruvate and ketone metabolism were up-regulated. Inter-ventricular significance of these metabolic pathways was then found to be diminished within end-stage dilated cardiomyopathy and ischaemic cardiomyopathy (n = 30-33), while heart failure-associated pathways were increased in the left ventricle relative to the right within ischaemic cardiomyopathy, such as fluid sheer-stress, increased glutamine to glutamate ratio, and down-regulation of contractile proteins indicating a left ventricular pathological bias.
Institute:The University of Sydney
Last Name:Hunter
First Name:Benjamin
Address:John Hopkins Dr, Camperdown, NSW, 2006, Australia
Email:benjamin.hunter@sydney.edu.au
Phone:+61422525639

Subject:

Subject ID:SU002822
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id LV/RV Condition Sex
SA273662Raw_SmpID_114LV DCM F
SA273663Raw_SmpID_112LV DCM F
SA273664Raw_SmpID_115LV DCM M
SA273665Raw_SmpID_113LV DCM M
SA273666Raw_SmpID_110LV DCM M
SA273667Raw_SmpID_111LV DCM M
SA273668Raw_SmpID_109LV DCM M
SA273669Raw_SmpID_126LV Donor F
SA273670Raw_SmpID_83LV Donor F
SA273671Raw_SmpID_117LV Donor F
SA273672Raw_SmpID_80LV Donor F
SA273673Raw_SmpID_118LV Donor F
SA273674Raw_SmpID_119LV Donor F
SA273675Raw_SmpID_122LV Donor F
SA273676Raw_SmpID_125LV Donor F
SA273677Raw_SmpID_78LV Donor F
SA273678Raw_SmpID_76LV Donor F
SA273679Raw_SmpID_123LV Donor M
SA273680Raw_SmpID_81LV Donor M
SA273681Raw_SmpID_116LV Donor M
SA273682Raw_SmpID_75LV Donor M
SA273683Raw_SmpID_120LV Donor M
SA273684Raw_SmpID_82LV Donor M
SA273685Raw_SmpID_84LV Donor M
SA273686Raw_SmpID_79LV Donor M
SA273687Raw_SmpID_77LV Donor M
SA273688Raw_SmpID_68LV ICM F
SA273689Raw_SmpID_106LV ICM F
SA273690Raw_SmpID_65LV ICM F
SA273691Raw_SmpID_72LV ICM F
SA273692Raw_SmpID_69LV ICM F
SA273693Raw_SmpID_66LV ICM F
SA273694Raw_SmpID_70LV ICM M
SA273695Raw_SmpID_71LV ICM M
SA273696Raw_SmpID_74LV ICM M
SA273697Raw_SmpID_67LV ICM M
SA273698Raw_SmpID_73LV ICM M
SA273699Raw_SmpID_107LV ICM M
SA273700Raw_SmpID_95RV Donor F
SA273701Raw_SmpID_121RV Donor F
SA273702Raw_SmpID_124RV Donor F
SA273703Raw_SmpID_98RV Donor F
SA273704Raw_SmpID_100RV Donor F
SA273705Raw_SmpID_101RV Donor F
SA273706Raw_SmpID_104RV Donor F
SA273707Raw_SmpID_96RV Donor M
SA273708Raw_SmpID_97RV Donor M
SA273709Raw_SmpID_102RV Donor M
SA273710Raw_SmpID_99RV Donor M
SA273711Raw_SmpID_103RV Donor M
SA273712Raw_SmpID_105RV Donor M
SA273713Raw_SmpID_88RV ICM F
SA273714Raw_SmpID_86RV ICM F
SA273715Raw_SmpID_85RV ICM F
SA273716Raw_SmpID_91RV ICM F
SA273717Raw_SmpID_93RV ICM F
SA273718Raw_SmpID_108RV ICM M
SA273719Raw_SmpID_94RV ICM M
SA273720Raw_SmpID_87RV ICM M
SA273721Raw_SmpID_92RV ICM M
SA273722Raw_SmpID_89RV ICM M
SA273723Raw_SmpID_90RV ICM M
Showing results 1 to 62 of 62

Collection:

Collection ID:CO002815
Collection Summary:Donated human myocardium. Refer to uploaded acquisition methods.
Collection Protocol Filename:LVvsRV_Tissue_aquisition_Methods.docx
Sample Type:Heart
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR002831
Treatment Summary:Human myocardial tissue from the left ventricle was compared to the right ventricle within three conditions; non-diseased donors, ischaemic cardiomyopathy, and dilated cardiomyopathy, but not between the different conditions.
Treatment Protocol Filename:LVvsRV_Metabolomics_Methods_2020.docx

Sample Preparation:

Sampleprep ID:SP002828
Sampleprep Summary:Refer to the uploaded methods file.
Sampleprep Protocol Filename:LVvsRV_Metabolomics_Methods_2020.docx

Combined analysis:

Analysis ID AN004405 AN004406
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1260 Agilent 1260
Column Waters Atlantis HILIC (150 x 2.1mm,3um) Waters XBridge Amide (100 x 2.1mm,3.5um)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap ABI Sciex 5500 QTrap
Ion Mode POSITIVE POSITIVE
Units Relative abundance Relative abundance

Chromatography:

Chromatography ID:CH003306
Chromatography Summary:HPLC gradient: The HPLC gradient program begins with an initial condition of 5% solvent A and 95% solvent B, with a flow rate of 0.25 mL/min, which is held for 0.5 minutes to establish system equilibration. The gradient then proceeds as follows: at 6 minutes, the mobile phase composition shifts to 60% solvent A and 40% solvent B for 3minutes; at 10 minutes, it changes back to 5% solvent A and 95% solvent B; at 11 minutes, the flow rate increases to 0.4 mL/min while maintaining a composition of 5% solvent A and 95% solvent B for a duration of 12.5 minutes; and at 24.5 minutes, the flow rate decreases back to 0.25 mL/min. The final condition is maintained for 1 minutes to ensure stability before subsequent analyses.
Instrument Name:Agilent 1260
Column Name:Waters Atlantis HILIC (150 x 2.1mm,3um)
Column Temperature:40°C
Flow Gradient:HPLC gradient: The HPLC gradient program begins with an initial condition of 5% solvent A and 95% solvent B, with a flow rate of 0.25 mL/min, which is held for 0.5 minutes to establish system equilibration. The gradient then proceeds as follows: at 6 minutes, the mobile phase composition shifts to 60% solvent A and 40% solvent B for 3minutes; at 10 minutes, it changes back to 5% solvent A and 95% solvent B; at 11 minutes, the flow rate increases to 0.4 mL/min while maintaining a composition of 5% solvent A and 95% solvent B for a duration of 12.5 minutes; and at 24.5 minutes, the flow rate decreases back to 0.25 mL/min.
Flow Rate:0.250 – 0.400 mL/min
Solvent A:0.1% Formic acid in 10 mM Ammonium Formate (pH ~2.5)
Solvent B:0.1% Formic Acid in Acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH003307
Chromatography Summary:HPLC gradient: The HPLC gradient program is initialized with an initial mobile phase composition of 15% solvent A and 85% solvent B at a flow rate of 0.25 mL/min. Over the course of 8 minutes, the mobile phase composition undergoes a transition to 65% solvent A and 35% solvent B. Subsequently, at 8 minutes, the composition shifts to 98% solvent A and 2% solvent B, maintained for 1 minute. The mobile phase reverts back to the initial composition of 15% solvent A and 85% solvent B at 10 minutes. At 12.5 minutes, the flow rate is increased to 0.5 mL/min, while maintaining a constant mobile phase composition of 15% solvent A and 85% solvent B for a period of 2.5 minutes. Finally, at 15 minutes, the flow rate is reduced back to 0.25 mL/min. To ensure system stability, the final condition is maintained for 1 minute prior to subsequent analyses.
Instrument Name:Agilent 1260
Column Name:Waters XBridge Amide (100 x 2.1mm,3.5um)
Column Temperature:40°C
Flow Gradient:HPLC gradient: The HPLC gradient program is initialized with an initial mobile phase composition of 15% solvent A and 85% solvent B at a flow rate of 0.25 mL/min. Over the course of 8 minutes, the mobile phase composition undergoes a transition to 65% solvent A and 35% solvent B. Subsequently, at 8 minutes, the composition shifts to 98% solvent A and 2% solvent B, maintained for 1 minute. The mobile phase reverts back to the initial composition of 15% solvent A and 85% solvent B at 10 minutes. At 12.5 minutes, the flow rate is increased to 0.5 mL/min, while maintaining a constant mobile phase composition of 15% solvent A and 85% solvent B for a period of 2.5 minutes.
Flow Rate:0.250 – 0.400 mL/min
Solvent A:95:5 H2O:Acetonitrile (v:v) with 20mM Ammonium Acetate and 20mM Ammonium Hydroxide (pH 9.0)
Solvent B:Acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS004154
Analysis ID:AN004405
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:The analysis software MultiQuant 3.0 (ABSciex) was used for MRM Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex).
Ion Mode:POSITIVE
Analysis Protocol File:LVvsRV_Metabolomics_Methods_2020.docx
  
MS ID:MS004155
Analysis ID:AN004406
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:The analysis software MultiQuant 3.0 (ABSciex) was used for MRM Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex).
Ion Mode:POSITIVE
Analysis Protocol File:LVvsRV_Metabolomics_Methods_2020.docx
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