Summary of Study ST002716

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.

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 IDST002716
Study TitleVentricle-specific myocardial protein and metabolite characterisation in healthy humans, with differential regulation in end-stage cardiomyopathies (Part 1)
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 Date2023-05-23
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

Select appropriate tab below to view additional metadata details:

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:SU002821
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 Location Condition
SA273598Raw_SmpID_48LV DCM
SA273599Raw_SmpID_50LV DCM
SA273600Raw_SmpID_60LV DCM
SA273601Raw_SmpID_58LV DCM
SA273602Raw_SmpID_51LV DCM
SA273603Raw_SmpID_49LV DCM
SA273604Raw_SmpID_57LV DCM
SA273605Raw_SmpID_61LV DCM
SA273606Raw_SmpID_56LV DCM
SA273607Raw_SmpID_47LV DCM
SA273608Raw_SmpID_59LV DCM
SA273609Raw_SmpID_63LV DCM
SA273610Raw_SmpID_62LV DCM
SA273611Raw_SmpID_21LV Donor
SA273612Raw_SmpID_15LV Donor
SA273613Raw_SmpID_14LV Donor
SA273614Raw_SmpID_22LV Donor
SA273615Raw_SmpID_2LV Donor
SA273616Raw_SmpID_8LV Donor
SA273617Raw_SmpID_16LV Donor
SA273618Raw_SmpID_9LV Donor
SA273619Raw_SmpID_11LV Donor
SA273620Raw_SmpID_6LV Donor
SA273621Raw_SmpID_19LV Donor
SA273622Raw_SmpID_20LV Donor
SA273623Raw_SmpID_18LV Donor
SA273624Raw_SmpID_17LV Donor
SA273625Raw_SmpID_10LV Donor
SA273626Raw_SmpID_7LV Donor
SA273627Raw_SmpID_3LV Donor
SA273628Raw_SmpID_13LV Donor
SA273629Raw_SmpID_1LV Donor
SA273630Raw_SmpID_12LV Donor
SA273631Raw_SmpID_4LV Donor
SA273632Raw_SmpID_5LV Donor
SA273633Raw_SmpID_37LV ICM
SA273634Raw_SmpID_27LV ICM
SA273635Raw_SmpID_29LV ICM
SA273636Raw_SmpID_32LV ICM
SA273637Raw_SmpID_33LV ICM
SA273638Raw_SmpID_39LV ICM
SA273639Raw_SmpID_30LV ICM
SA273640Raw_SmpID_41LV ICM
SA273641Raw_SmpID_35LV ICM
SA273642Raw_SmpID_40LV ICM
SA273643Raw_SmpID_31LV ICM
SA273644Raw_SmpID_34LV ICM
SA273645Raw_SmpID_36LV ICM
SA273646Raw_SmpID_38LV ICM
SA273647Raw_SmpID_46LV ICM
SA273648Raw_SmpID_28LV ICM
SA273649Raw_SmpID_54RV DCM
SA273650Raw_SmpID_55RV DCM
SA273651Raw_SmpID_52RV DCM
SA273652Raw_SmpID_53RV DCM
SA273653Raw_SmpID_64RV DCM
SA273654Raw_SmpID_24RV Donor
SA273655Raw_SmpID_25RV Donor
SA273656Raw_SmpID_23RV Donor
SA273657Raw_SmpID_26RV Donor
SA273658Raw_SmpID_42RV ICM
SA273659Raw_SmpID_45RV ICM
SA273660Raw_SmpID_43RV ICM
SA273661Raw_SmpID_44RV ICM
Showing results 1 to 64 of 64

Collection:

Collection ID:CO002814
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:TR002830
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_2018.docx

Sample Preparation:

Sampleprep ID:SP002827
Sampleprep Summary:Refer to the uploaded methods file.
Sampleprep Protocol Filename:LVvsRV_Metabolomics_Methods_2018.docx

Combined analysis:

Analysis ID AN004403 AN004404
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:CH003304
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:CH003305
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:MS004152
Analysis ID:AN004403
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_2018.docx
  
MS ID:MS004153
Analysis ID:AN004404
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_2018.docx
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