Summary of Study ST003104
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 PR001927. The data can be accessed directly via it's Project DOI: 10.21228/M8N42X 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 | ST003104 |
| Study Title | Metabolomics studies on human cardiac samples |
| Study Summary | Targeted metabolomics was performed to measure polar metabolites in both positive and negative ionization mode on left ventricular tissue acquired from pre-mortem healthy donor hearts as classified by formal pathological examination and stored at the Sydney Heart Bank. The minimum number of observations for young (age ≤ 25 years) and old (age ≥ 50 years) cohorts using liquid chromatography-tandem mass spectrometry (LC-MS/MS). |
| Institute | University of Sydney |
| Department | Medicine and Health |
| Last Name | Koay |
| First Name | Yen Chin |
| Address | Charles Perkin Centre |
| yen.koay@sydney.edu.au | |
| Phone | +61486275851 |
| Submit Date | 2023-09-10 |
| Num Groups | 2 |
| Total Subjects | 25 |
| Num Males | 15 |
| Num Females | 10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | API |
| Release Date | 2024-03-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001927 |
| Project DOI: | doi: 10.21228/M8N42X |
| Project Title: | The Human Cardiac “Age-OME”: Age-specific changes in myocardial molecular expression |
| Project Type: | MS analysis |
| Project Summary: | A substantial proportion of the World’s population is ageing. One of the most significant risk factors for heart disease is ageing. However, we do not understand how the human heart changes with age. Taking advantage of a unique set of pre-mortem, cryopreserved, non-diseased human hearts, we performed multi-omic analyses (transcriptomics, proteomics, metabolomics and lipidomics), coupled with biological computational modelling in younger (<25 years old) and older hearts (>50years old) to describe the molecular landscape of human cardiac ageing. In older hearts, we observed a downregulation of proteins involved in calcium signalling and of the contractile apparatus itself. In addition, we found a potential counteractive upregulation of central carbon generation of fuel, upregulation of glycolysis and increases in long-chain fatty acids. This is the first molecular data set of normal human cardiac ageing, which may have important implications for the development of age-related heart disease. |
| Institute: | University of Sydney |
| Department: | School of Medical Sciences |
| Laboratory: | Cardiometabolic Medicine |
| Last Name: | Koay |
| First Name: | Yen Chin |
| Address: | The Hub, Charles Perkins Centre, D17, The University of Sydney, NSW, 2006 |
| Email: | yen.koay@sydney.edu.au |
| Phone: | +61486275851 |
Subject:
| Subject ID: | SU003219 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | Young donors (aged 25 years or younger) and older donors (aged 50 years or older). |
| Gender: | Male and female |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Group | Sex |
|---|---|---|---|---|
| SA333595 | old_6 | heart tissue | Old | Female |
| SA333596 | old_5 | heart tissue | Old | Female |
| SA333597 | old_7 | heart tissue | Old | Female |
| SA333598 | old_11 | heart tissue | Old | Female |
| SA333599 | old_13 | heart tissue | Old | Female |
| SA333600 | old_3 | heart tissue | Old | Female |
| SA333601 | old_1 | heart tissue | Old | Female |
| SA333602 | old_8 | heart tissue | Old | Male |
| SA333603 | old_2 | heart tissue | Old | Male |
| SA333604 | old_9 | heart tissue | Old | Male |
| SA333605 | old_10 | heart tissue | Old | Male |
| SA333606 | old_12 | heart tissue | Old | Male |
| SA333607 | old_4 | heart tissue | Old | Male |
| SA333608 | young_7 | heart tissue | Young | Female |
| SA333609 | young_10 | heart tissue | Young | Female |
| SA333610 | young_12 | heart tissue | Young | Female |
| SA333611 | young_9 | heart tissue | Young | Male |
| SA333612 | young_3 | heart tissue | Young | Male |
| SA333613 | young_2 | heart tissue | Young | Male |
| SA333614 | young_4 | heart tissue | Young | Male |
| SA333615 | young_11 | heart tissue | Young | Male |
| SA333616 | young_5 | heart tissue | Young | Male |
| SA333617 | young_1 | heart tissue | Young | Male |
| SA333618 | young_8 | heart tissue | Young | Male |
| SA333619 | young_6 | heart tissue | Young | Male |
| Showing results 1 to 25 of 25 |
Collection:
| Collection ID: | CO003212 |
| Collection Summary: | Control donor hearts that were considered suitable for transplantation but ultimately not used due to factors such as transport issues, immune mismatches, and size discrepancies between donor and recipient, rather than being post-mortem specimens were collected in this study. These hearts came from individuals who died of non-cardiac reasons and had no risk factors for heart disease, including having a BMI under 30. Following a thorough pathological review, these hearts were confirmed to be structurally normal through histological evaluation. Left ventricular (LV) samples were taken directly in the operating room, immediately snap-frozen in liquid nitrogen at -196°C, and then stored at the Sydney Heart Bank at the University of Sydney, at temperatures ranging from -170 to -180°C. This collection process received the ethical green light from the University of Sydney's Ethics Committee (USYD # 2021/122). |
| Sample Type: | Heart |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR003228 |
| Treatment Summary: | The samples detailed in this study did not undergo any treatment. |
Sample Preparation:
| Sampleprep ID: | SP003225 |
| Sampleprep Summary: | Briefly, approximately 50 mg of ground heart tissue was weighed into 2 mL Eppendorf tube and subjected to a two-phase extraction protocol involving tissue, ice-cold extraction medium (methanol:water, and chloroform). Samples were then centrifuged at 14 300 rpm at 4 °C for 25 min. The aqueous layer was transferred into a new microfuge tube, concentrated in the Speed-Vac SPD120 (Thermo Fisher Scientific) and dried under nitrogen stream, followed by reconstitution in the acetonitrile/methanol/formic acid (75:25:0.2; v/v/v, HPLC grade; Thermo Fisher Scientific) for the HILIC analysis, and acetonitrile/methanol (25:25; v/v/v, HPLC grade) for the AMIDE analysis. |
Combined analysis:
| Analysis ID | AN005082 | AN005083 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Agilent 1260 | Agilent 1260 |
| Column | Waters Atlantis T3 (150 x 4.6mm,5um) | Waters XBridge BEH Amide (100 x 2.1mm,2.5um) |
| MS Type | API | API |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 5500 QTrap | ABI Sciex 5500 QTrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | abundance | abundance |
Chromatography:
| Chromatography ID: | CH003839 |
| Chromatography Summary: | Chromatographic method to detect analytes such as amino acids, endocannabinoids, fatty acid β-oxidation intermediates, gut-derived metabolites, nucleotides, neurotransmitters, cofactors and vitamins. |
| Instrument Name: | Agilent 1260 |
| Column Name: | Waters Atlantis T3 (150 x 4.6mm,5um) |
| Column Temperature: | 40 |
| Flow Gradient: | The LC 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. |
| Flow Rate: | 0.250 – 0.400 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate (pH ~2.5) |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003840 |
| Chromatography Summary: | Chromatographic method to detect analytes including amino acids, nucleotides, nucleosides, nucleotide triphosphates, high energy intermediates, organic acids, TCA cycle intermediates, bile acids and vitamins. |
| Instrument Name: | Agilent 1260 |
| Column Name: | Waters XBridge BEH Amide (100 x 2.1mm,2.5um) |
| Column Temperature: | 40 |
| Flow Gradient: | The LC 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. |
| Flow Rate: | 0.250 – 0.400 mL/min |
| Solvent A: | 95% acetonitrile/5%; water 20mM ammonium acetate; 20mM ammonium hydroxide (pH 9.0) |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004820 |
| Analysis ID: | AN005082 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | API |
| MS Comments: | Targeted metabolite profiling was performed using MS multiple reaction-monitoring transitions. Multiple Reaction Monitoring (MRM) Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex) was performed using software MultiQuant 3.0 (ABSciex). |
| Ion Mode: | POSITIVE |
| MS ID: | MS004821 |
| Analysis ID: | AN005083 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | API |
| MS Comments: | Targeted metabolite profiling was performed using MS multiple reaction-monitoring transitions. Multiple Reaction Monitoring (MRM) Q1/Q3 peak integration of the raw data files (Analyst software, v.1.6.2; ABSciex) was performed using software MultiQuant 3.0 (ABSciex). |
| Ion Mode: | NEGATIVE |
