Summary of Study ST001907
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 PR001201. The data can be accessed directly via it's Project DOI: 10.21228/M8G69Q 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 | ST001907 |
| Study Title | Training-induced bioenergetic improvement in human skeletal muscle is associated with non-stoichiometric changes in the mitochondrial proteome without reorganisation of respiratory chain content |
| Study Type | Multi Omics |
| Study Summary | Lipidomic analysis of muscle mitochondrial isolates. 10 men with repeated measures. |
| Institute | Baker Heart and Diabetes Institute |
| Department | Meteabolomics |
| Laboratory | Meteabolomics |
| Last Name | Huynh |
| First Name | Kevin |
| Address | 75 Commercial Road |
| kevin.huynh@baker.edu.au | |
| Phone | 0385321537 |
| Submit Date | 2021-08-15 |
| Num Groups | 1 |
| Total Subjects | 10 |
| Num Males | 10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-10-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001201 |
| Project DOI: | doi: 10.21228/M8G69Q |
| Project Title: | Training-induced bioenergetic improvement in human skeletal muscle is associated with non-stoichiometric changes in the mitochondrial proteome without reorganisation of respiratory chain content |
| Project Type: | Multi-omics |
| Project Summary: | Defects in mitochondria have been implicated in multiple diseases and aging. Interventions to improve mitochondrial function have the potential to improve quality of life. Exercise training is a readily accessible and inexpensive intervention, however how it promotes mitochondrial adaptation in skeletal muscle remains poorly understood. Here, we describe an intricate and previously undemonstrated network of differentially prioritised training-induced adaptations in human skeletal muscle mitochondria. We show that changes in hundreds of transcripts, proteins and lipid species are not stoichiometrically linked to the increase in mitochondrial content. We demonstrate a prioritization of specific pathways at different stages of the intervention, including initial deprioritisation of oxidative phosphorylation (OXPHOS) and prioritisation of TCA cycle and fatty acid β-oxidation linked mitochondrial respiration. This indicates that enhancing electron flow to OXPHOS is more important to increase ATP production than increasing the abundance of the OXPHOS machinery. Our research unearths the elaborate and multi-layered nature of the adaptive response to exercise and provides a valuable resource that can be mined to maximise the therapeutic benefits of exercise. |
| Institute: | Baker Heart and Diabetes Institute |
| Department: | Baker Heart and Diabetes Institute |
| Laboratory: | Metabolomics |
| Last Name: | Huynh |
| First Name: | Kevin |
| Address: | 75 Commercial Road |
| Email: | kevin.huynh@baker.edu.au |
| Phone: | 0385321537 |
Subject:
| Subject ID: | SU001985 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | ID |
|---|---|---|
| SA176734 | 10NK-1 | 0N |
| SA176735 | 10NK-2 | 0N |
| SA176736 | 10NK-8 | 0N |
| SA176737 | 10NK-5 | 0N |
| SA176738 | 12JP-8 | 2J |
| SA176739 | 12JP-2 | 2J |
| SA176740 | 12JP-1 | 2J |
| SA176741 | 12JP-5 | 2J |
| SA176742 | 13AP-1 | 3A |
| SA176743 | 13AP-5 | 3A |
| SA176744 | 13AP-8 | 3A |
| SA176745 | 13AP-2 | 3A |
| SA176746 | 14EP-8 | 4E |
| SA176747 | 14EP-1 | 4E |
| SA176748 | 14EP-2 | 4E |
| SA176749 | 14EP-5 | 4E |
| SA176750 | 1AM-2 | AM |
| SA176751 | 1AM-5 | AM |
| SA176752 | 1AM-1 | AM |
| SA176753 | 1AM-8 | AM |
| SA176754 | 5CP-2 | CP |
| SA176755 | 5CP-1 | CP |
| SA176756 | 5CP-8 | CP |
| SA176757 | 5CP-5 | CP |
| SA176758 | 9GG-1 | GG |
| SA176759 | 9GG-2 | GG |
| SA176760 | 9GG-5 | GG |
| SA176761 | 9GG-8 | GG |
| SA176762 | 7SL-8 | SL |
| SA176763 | 7SL-1 | SL |
| SA176764 | 7SL-5 | SL |
| SA176765 | 7SL-2 | SL |
| SA176766 | 4SR-2 | SR |
| SA176767 | 4SR-8 | SR |
| SA176768 | 4SR-1 | SR |
| SA176769 | 4SR-5 | SR |
| SA176770 | 6WP-2 | WP |
| SA176771 | 6WP-8 | WP |
| SA176772 | 6WP-1 | WP |
| SA176773 | 6WP-5 | WP |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO001978 |
| Collection Summary: | Muscle biopsies. A biopsy needle with suction under local anaesthesia (1% xylocaine) was 688 used to obtain vastus lateralis muscle biopsies at rest at the following four time points: BL, 689 PN, PH and PR. After being cleaned of excess blood, connective and fat tissue muscle 690 biopsies were divided as follows: ~10 mg was immediately immersed in ~2 mL of ice-cold 691 BIOPS for measurements of mitochondrial respiration, whereas the remainder was promptly 692 frozen in liquid nitrogen and stored at -80°C for follow-up analyses. |
| Sample Type: | Muscle |
Treatment:
| Treatment ID: | TR001997 |
| Treatment Summary: | Training intervention. All training sessions were performed on an electronically braked cycle ergometer (Velotron, RacerMate, USA), following an 8-min warm up (see 20k-TT) and consisted of HIIT (2:1 work-to-rest ratio). Training intensity was set relative to ẆLT (rather than ẆPeak) so as to induce similar metabolic and cardiac stresses amongst participants of differing fitness levels75. Exercise intensity was maintained between ẆLT and ẆPeak throughout the entire study so that training volume was the only manipulated variable between the 3 phases. NVT phase. This consisted of 6 HIIT sessions within 2 weeks of 5 to 7 4-min cycling intervals interspersed with a 2-min recovery at 60 W. Exercise intensities were defined as [ẆLT + x(ẆPeak-ẆLT)], with x increasing from 0.5 to 0.7 throughout the phase. HVT phase. Participants performed HIIT twice a day for 20 consecutive days; training sessions consisted of either 7 to 10 4-min intervals interspersed with a 2-min recovery at 60 W at intensities ranging from [ẆLT + 0.5(ẆPeak-ẆLT)] to [ẆLT + 0.8(ẆPeak-ẆLT)], or 15 to 20 2-min intervals at intensities ranging from [ẆLT + 0.5(ẆPeak-ẆLT)] to [ẆLT + 0.95(ẆPeak-ẆLT)], interspersed with a 1-min recovery at 60 W. Single session duration increased from ~45 min to 60 min. RVT phase. The RVT phase consisted of 6 HIIT sessions in 6 days; participants performed 10, 9, 8, 7, 6, and 4, 4-min intervals interspersed with a 2-min recovery at 60 W, at an intensity of [ẆLT + x(ẆPeak- ẆLT)], with x increasing from 0.5 to 0.7 throughout the phase. |
Sample Preparation:
| Sampleprep ID: | SP001991 |
| Sampleprep Summary: | Mitochondrial isolates were extracted using a modified single-phase chloroform/methanol extraction as described previously (Weir et al. 2013). In brief, 20 volumes of chloroform:methanol (2:1) were added to the sample along with a series of internal standards. Samples were vortexed and centrifuged on a rotary mixer for 10 min. Following sonication on a sonicator bath for 30 min, samples were rested for 20 min prior to centrifugation at 13,000 g for 10 min. Supernatants were transferred into a 96 well plated, dried down and reconstituted in 50 μL H2O saturated butanol and sonicated for 10 min. After the addition of 50 μL of methanol with 10 mM ammonium 945 formate, samples were centrifuged at 4000 rpm on a plate centrifuge and transferred into glass vials with inserts for mass spectrometry analysis. |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Single phase 2:1 chloroform methanol |
| Extract Storage: | -80℃ |
| Sample Resuspension: | Butanol : Methanol 1:1 |
| Subcellular Location: | Mitochondria |
Combined analysis:
| Analysis ID | AN003104 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II |
| Column | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ |
| Ion Mode | POSITIVE |
| Units | pmol per mg |
Chromatography:
| Chromatography ID: | CH002291 |
| Chromatography Summary: | The running solvent consisted of solvent A: 50% H2O / 30% acetonitrile / 20% isopropanol (v/v/v) containing 10mM ammonium formate and 5uM medronic acid, and solvent B: 1% H2O / 9% acetonitrile / 90% isopropanol (v/v/v) containing 10mM ammonium formate. We utilized a stepped linear gradient with a 16-minute cycle time per sample and a 1µL sample injection. To increase throughput, we used a dual column set up to equilibrate the second column while the first is running a sample. The sample analytical gradient was as follows: starting with a flow rate of 0.4mL/minute at 15% B and increasing to 50% B over 2.5 minutes, then to 57% over 0.1 minutes, to 70% over 6.4 minutes, to 93% over 0.1 minute, to 96% over 1.9 minutes and finally to 100% over 0.1 minute. The solvent was then held at 100% B for 0.9 minutes (total 12.0 minutes). Equilibration was started as follows: solvent was decreased from 100% B to 15% B over 0.2 minutes and held until a total of 16 minutes. The next sample is injected and the columns are switched. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um) |
| Flow Gradient: | starting with a flow rate of 0.4mL/minute at 15% B and increasing to 50% B over 2.5 minutes, then to 57% over 0.1 minutes, to 70% over 6.4 minutes, to 93% over 0.1 minute, to 96% over 1.9 minutes and finally to 100% over 0.1 minute. The solvent was then held at 100% B for 0.9 minutes (total 12.0 minutes). Equilibration was started as follows: solvent was decreased from 100% B to 15% B over 0.2 minutes and held until a total of 16 minutes. |
| Flow Rate: | 0.4mL/min |
| Solvent A: | 50% water/30% acetonitrile/20% isopropanol; 10mM ammonium formate; 5uM medronic acid |
| Solvent B: | 1% water/9% acetonitrile/90% isopropanol; 10mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002886 |
| Analysis ID: | AN003104 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Details previously published in https://doi.org/10.1016/j.chembiol.2018.10.008 |
| Ion Mode: | POSITIVE |
