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.
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.
| Study ID | ST002717 |
| Study Title | Ventricle-specific myocardial protein and metabolite characterisation in healthy humans, with differential regulation in end-stage cardiomyopathies (Part 2) |
| Study 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 | University of Sydney |
| Last Name | Hunter |
| First Name | Benjamin |
| Address | John Hopkins Dr, Camperdown, NSW, 2006, Australia |
| benjamin.hunter@sydney.edu.au | |
| Phone | +61422525639 |
| Submit Date | 2023-05-25 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-06-27 |
| Release Version | 1 |
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: | 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 |
|---|---|---|
| SA273662 | Raw_SmpID_114 | LV | Condition:DCM | Sex:F |
| SA273663 | Raw_SmpID_112 | LV | Condition:DCM | Sex:F |
| SA273664 | Raw_SmpID_115 | LV | Condition:DCM | Sex:M |
| SA273665 | Raw_SmpID_113 | LV | Condition:DCM | Sex:M |
| SA273666 | Raw_SmpID_110 | LV | Condition:DCM | Sex:M |
| SA273667 | Raw_SmpID_111 | LV | Condition:DCM | Sex:M |
| SA273668 | Raw_SmpID_109 | LV | Condition:DCM | Sex:M |
| SA273669 | Raw_SmpID_126 | LV | Condition:Donor | Sex:F |
| SA273670 | Raw_SmpID_83 | LV | Condition:Donor | Sex:F |
| SA273671 | Raw_SmpID_117 | LV | Condition:Donor | Sex:F |
| SA273672 | Raw_SmpID_80 | LV | Condition:Donor | Sex:F |
| SA273673 | Raw_SmpID_118 | LV | Condition:Donor | Sex:F |
| SA273674 | Raw_SmpID_119 | LV | Condition:Donor | Sex:F |
| SA273675 | Raw_SmpID_122 | LV | Condition:Donor | Sex:F |
| SA273676 | Raw_SmpID_125 | LV | Condition:Donor | Sex:F |
| SA273677 | Raw_SmpID_78 | LV | Condition:Donor | Sex:F |
| SA273678 | Raw_SmpID_76 | LV | Condition:Donor | Sex:F |
| SA273679 | Raw_SmpID_123 | LV | Condition:Donor | Sex:M |
| SA273680 | Raw_SmpID_81 | LV | Condition:Donor | Sex:M |
| SA273681 | Raw_SmpID_116 | LV | Condition:Donor | Sex:M |
| SA273682 | Raw_SmpID_75 | LV | Condition:Donor | Sex:M |
| SA273683 | Raw_SmpID_120 | LV | Condition:Donor | Sex:M |
| SA273684 | Raw_SmpID_82 | LV | Condition:Donor | Sex:M |
| SA273685 | Raw_SmpID_84 | LV | Condition:Donor | Sex:M |
| SA273686 | Raw_SmpID_79 | LV | Condition:Donor | Sex:M |
| SA273687 | Raw_SmpID_77 | LV | Condition:Donor | Sex:M |
| SA273688 | Raw_SmpID_68 | LV | Condition:ICM | Sex:F |
| SA273689 | Raw_SmpID_106 | LV | Condition:ICM | Sex:F |
| SA273690 | Raw_SmpID_65 | LV | Condition:ICM | Sex:F |
| SA273691 | Raw_SmpID_72 | LV | Condition:ICM | Sex:F |
| SA273692 | Raw_SmpID_69 | LV | Condition:ICM | Sex:F |
| SA273693 | Raw_SmpID_66 | LV | Condition:ICM | Sex:F |
| SA273694 | Raw_SmpID_70 | LV | Condition:ICM | Sex:M |
| SA273695 | Raw_SmpID_71 | LV | Condition:ICM | Sex:M |
| SA273696 | Raw_SmpID_74 | LV | Condition:ICM | Sex:M |
| SA273697 | Raw_SmpID_67 | LV | Condition:ICM | Sex:M |
| SA273698 | Raw_SmpID_73 | LV | Condition:ICM | Sex:M |
| SA273699 | Raw_SmpID_107 | LV | Condition:ICM | Sex:M |
| SA273700 | Raw_SmpID_95 | RV | Condition:Donor | Sex:F |
| SA273701 | Raw_SmpID_121 | RV | Condition:Donor | Sex:F |
| SA273702 | Raw_SmpID_124 | RV | Condition:Donor | Sex:F |
| SA273703 | Raw_SmpID_98 | RV | Condition:Donor | Sex:F |
| SA273704 | Raw_SmpID_100 | RV | Condition:Donor | Sex:F |
| SA273705 | Raw_SmpID_101 | RV | Condition:Donor | Sex:F |
| SA273706 | Raw_SmpID_104 | RV | Condition:Donor | Sex:F |
| SA273707 | Raw_SmpID_96 | RV | Condition:Donor | Sex:M |
| SA273708 | Raw_SmpID_97 | RV | Condition:Donor | Sex:M |
| SA273709 | Raw_SmpID_102 | RV | Condition:Donor | Sex:M |
| SA273710 | Raw_SmpID_99 | RV | Condition:Donor | Sex:M |
| SA273711 | Raw_SmpID_103 | RV | Condition:Donor | Sex:M |
| SA273712 | Raw_SmpID_105 | RV | Condition:Donor | Sex:M |
| SA273713 | Raw_SmpID_88 | RV | Condition:ICM | Sex:F |
| SA273714 | Raw_SmpID_86 | RV | Condition:ICM | Sex:F |
| SA273715 | Raw_SmpID_85 | RV | Condition:ICM | Sex:F |
| SA273716 | Raw_SmpID_91 | RV | Condition:ICM | Sex:F |
| SA273717 | Raw_SmpID_93 | RV | Condition:ICM | Sex:F |
| SA273718 | Raw_SmpID_108 | RV | Condition:ICM | Sex:M |
| SA273719 | Raw_SmpID_94 | RV | Condition:ICM | Sex:M |
| SA273720 | Raw_SmpID_87 | RV | Condition:ICM | Sex:M |
| SA273721 | Raw_SmpID_92 | RV | Condition:ICM | Sex:M |
| SA273722 | Raw_SmpID_89 | RV | Condition:ICM | Sex:M |
| SA273723 | Raw_SmpID_90 | RV | Condition:ICM | Sex: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 | QTRAP | QTRAP |
| 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: | QTRAP |
| 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: | QTRAP |
| 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 |
