Summary of Study ST002183
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 PR001390. The data can be accessed directly via it's Project DOI: 10.21228/M82117 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 | ST002183 |
| Study Title | Individualized exercise intervention for people with multiple myeloma improves quality of life in a randomized controlled trial |
| Study Summary | Although new treatments have improved survival for multiple myeloma (MM), quality of life remains poor for people with this incurable cancer. We conducted a multi-site randomized, waitlist-controlled trial of an individualized exercise program for people at all stages of MM (n=60). Compared to the waitlist control group, participants of the 12-week intervention had significant improvement in health-related quality of life, mediated through improved MM symptoms, cardiorespiratory fitness and bone pain, with were mostly maintained at follow-up (up to 12 months). Exploratory plasma metabolomics and lipidomics was conducted to delineate molecular mechanisms and biomarkers |
| Institute | QIMR Berghofer Medical Research Institute |
| Laboratory | Precision & Systems Biomedicine |
| Last Name | Stoll |
| First Name | Thomas |
| Address | 300 Herston Road |
| thomas.stoll@qimrberghofer.edu.au | |
| Phone | +61 7 3845 3992 |
| Submit Date | 2022-06-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-02-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003575 | AN003576 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | HILIC |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1 mm,1.8 µm | Agilent Poroshell 120 HILIC-Z (100 2.1mm,2.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6545 QTOF | Agilent 6545 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
MS:
| MS ID: | MS003332 |
| Analysis ID: | AN003575 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | MS acquisition: Full scan MS data acquisition (m/z 50-1700) was carried out at a scan rate of 2.5 spectra/sec with the following source conditions applied for metabolites analysed on reversed-phase: Gas temperature 250°C, gas flow 13 L/min, sheath gas temperature and flow at 400°C and 12 L/min, respectively, nebulizer 30 psi, fragmentor 135, capillary voltage at +4500 V, nozzle voltage and CE were zero. For metabolite separation on HILIC conditions were adjusted as follows: Gas temperature 200°C, gas flow 10 L/min, nebulizer 40 psi, capillary voltage at -2500 V. MS/MS acquisition: For compound identification, the ‘Iterative MS/MS’ data acquisition mode was employed, i.e. a sample (here: QC pools) was injected multiple times and precursors previously selected for MS/MS fragmentation were excluded in subsequent runs. Eight iterative MS/MS acquisition runs per fixed collision energy (CE) value were performed with CE values set to 0, 10, 20, and 40 V. Spectral parameters were as follows: MS and MS/MS mass range was 50-1700; MS and MS/MS acquisition rate was 3 spectra/sec; quadrupole isolation width was narrow (~1.3 m/z). A maximum of 8 precursors per cycle were targeted which resulted in a cycle time of 3.1 s. Precursor threshold was set to 500 counts or 0.001% with an active exclusion of 0.2 min after 1 spectra. Iterative MS/MS settings were enabled with a mass error tolerance of +/- 5 ppm and retention time exclusion tolerance of +/- 0.1 min. Precursor charge state was set to 1, 2 and unknown. Precursor abundance-based scan speed with a target of 25,000 counts/spectrum and the use MS/MS accumulation time limit were enabled. Precursor purity stringency was kept at 70% and cutoff 0%. Reference ions were excluded from fragmentation with a delta mass tolerance of 10 ppm. Data processing: Feature extraction was performed separately for each of the 2 LC/MS analysis modes. A total of 148 data files (126 patient samples, 16 QCs, and 6 blank negative control extractions) were loaded into MassHunter Profinder (v 10 SP1, Agilent) and assigned to sample groups. Patient samples were divided into 2 sample groups (waitlist and exercise group), totalling 4 samples groups altogether. First, retention time alignment was conducted using a QC run as reference file. Spectral feature extraction was then performed using the recursive feature extraction method employing default settings with minor adjustments: Peak extraction retention time (Rt) range was restricted to 0.1-5 min and 0.1-7 min for reversed-phase and HILIC, respectively, compound binning and alignment tolerances were set to 1% + 0.3 min for Rt and 20 ppm + 2 mDa for mass, integrator Agile 2 was used for peak integration, peak filters were set to at least 2500 counts and features must have satisfied filter conditions in at least 75 % of files in at least one sample group. Feature peak area was exported and data cleaning was performed in accordance with Southam et al. (2021) using an in-house R script compiled of the following steps. QC samples were removed from the data matrix area if the total peak area (of all features) exceeded +/-25% of the median QC total peak area. Features were deleted from the data matrix if: detected in less than 70% of QC samples; absent across all sample groups; the mean QC/extract blank area ratio was less than 5; and the peak area RSD across QC samples was larger than 30%. In addition, duplicate feature entries were removed. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003333 |
| Analysis ID: | AN003576 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | MS acquisition: Full scan MS data acquisition (m/z 50-1700) was carried out at a scan rate of 2.5 spectra/sec with the following source conditions applied for metabolites analysed on reversed-phase: Gas temperature 250°C, gas flow 13 L/min, sheath gas temperature and flow at 400°C and 12 L/min, respectively, nebulizer 30 psi, fragmentor 135, capillary voltage at +4500 V, nozzle voltage and CE were zero. For metabolite separation on HILIC conditions were adjusted as follows: Gas temperature 200°C, gas flow 10 L/min, nebulizer 40 psi, capillary voltage at -2500 V. MS/MS acquisition: For compound identification, the ‘Iterative MS/MS’ data acquisition mode was employed, i.e. a sample (here: QC pools) was injected multiple times and precursors previously selected for MS/MS fragmentation were excluded in subsequent runs. Eight iterative MS/MS acquisition runs per fixed collision energy (CE) value were performed with CE values set to 0, 10, 20, and 40 V. Spectral parameters were as follows: MS and MS/MS mass range was 50-1700; MS and MS/MS acquisition rate was 3 spectra/sec; quadrupole isolation width was narrow (~1.3 m/z). A maximum of 8 precursors per cycle were targeted which resulted in a cycle time of 3.1 s. Precursor threshold was set to 500 counts or 0.001% with an active exclusion of 0.2 min after 1 spectra. Iterative MS/MS settings were enabled with a mass error tolerance of +/- 5 ppm and retention time exclusion tolerance of +/- 0.1 min. Precursor charge state was set to 1, 2 and unknown. Precursor abundance-based scan speed with a target of 25,000 counts/spectrum and the use MS/MS accumulation time limit were enabled. Precursor purity stringency was kept at 70% and cutoff 0%. Reference ions were excluded from fragmentation with a delta mass tolerance of 10 ppm. Data processing: Feature extraction was performed separately for each of the 2 LC/MS analysis modes. A total of 148 data files (126 patient samples, 16 QCs, and 6 blank negative control extractions) were loaded into MassHunter Profinder (v 10 SP1, Agilent) and assigned to sample groups. Patient samples were divided into 2 sample groups (waitlist and exercise group), totalling 4 samples groups altogether. First, retention time alignment was conducted using a QC run as reference file. Spectral feature extraction was then performed using the recursive feature extraction method employing default settings with minor adjustments: Peak extraction retention time (Rt) range was restricted to 0.1-5 min and 0.1-7 min for reversed-phase and HILIC, respectively, compound binning and alignment tolerances were set to 1% + 0.3 min for Rt and 20 ppm + 2 mDa for mass, integrator Agile 2 was used for peak integration, peak filters were set to at least 2500 counts and features must have satisfied filter conditions in at least 75 % of files in at least one sample group. Feature peak area was exported and data cleaning was performed in accordance with Southam et al. (2021) using an in-house R script compiled of the following steps. QC samples were removed from the data matrix area if the total peak area (of all features) exceeded +/-25% of the median QC total peak area. Features were deleted from the data matrix if: detected in less than 70% of QC samples; absent across all sample groups; the mean QC/extract blank area ratio was less than 5; and the peak area RSD across QC samples was larger than 30%. In addition, duplicate feature entries were removed. |
| Ion Mode: | NEGATIVE |
