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.

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Study IDST002183
Study TitleIndividualized exercise intervention for people with multiple myeloma improves quality of life in a randomized controlled trial
Study SummaryAlthough 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
LaboratoryPrecision & Systems Biomedicine
Last NameStoll
First NameThomas
Address300 Herston Road
Emailthomas.stoll@qimrberghofer.edu.au
Phone+61 7 3845 3992
Submit Date2022-06-01
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-02-05
Release Version1
Thomas Stoll Thomas Stoll
https://dx.doi.org/10.21228/M82117
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001390
Project DOI:doi: 10.21228/M82117
Project Title:Individualized exercise intervention for people with multiple myeloma improves quality of life in a randomized controlled trial
Project Type:MS untargeted metabolomics analysis
Project 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, Herston, Queensland, 4006, Australia
Email:thomas.stoll@qimrberghofer.edu.au
Phone:+61 7 3845 3992

Subject:

Subject ID:SU002269
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Group Time_point
SA209692HP_BlankNegControlExtraction_04Blank Blank
SA209693HP_BlankNegControlExtraction_03Blank Blank
SA209694HP_BlankNegControlExtraction_01Blank Blank
SA209695HP_BlankNegControlExtraction_06Blank Blank
SA209696HP_BlankNegControlExtraction_02Blank Blank
SA209697HP_BlankNegControlExtraction_05Blank Blank
SA209746MM036_0_pE1exercise -
SA209747MM055_0_pE1exercise -
SA209748MM040_0_pE1exercise -
SA209749MM051_0_pE1exercise -
SA209750MM050_0_pE1exercise -
SA209751MM044_0_pE1exercise -
SA209752MM039_0_pE1exercise -
SA209753MM032_0_pE1exercise -
SA209754MM058_0_pE1exercise -
SA209755MM041_0_pE1exercise -
SA209756MM035_0_pE1exercise -
SA209757MM022_0_pE1exercise -
SA209758MM003_0_p1exercise -
SA209759MM014_0_p1exercise -
SA209760MM008_0_p1exercise -
SA209761MM011_0_p1exercise -
SA209762MM004_0_p1exercise -
SA209763MM010_0_p1exercise -
SA209764MM027_0_pE1exercise -
SA209765MM026_0_pE1exercise -
SA209766MM058_1_pE1exercise 1
SA209767MM051_1_pE1exercise 1
SA209768MM050_1_pE1exercise 1
SA209769MM036_1_pE1exercise 1
SA209770MM055_1_pE1exercise 1
SA209771MM041_1_pE1exercise 1
SA209772MM044_1_pE1exercise 1
SA209773MM040_1_pE1exercise 1
SA209774MM039_1_pE1exercise 1
SA209775MM022_1_pE1exercise 1
SA209776MM008_1_pE1exercise 1
SA209777MM010_1_pE1exercise 1
SA209778MM032_1_pE1exercise 1
SA209779MM014_1_pE1exercise 1
SA209780MM011_1_pE1exercise 1
SA209781MM035_1_pE1exercise 1
SA209782MM027_1_pE1exercise 1
SA209783MM003_1_pE1exercise 1
SA209784MM026_1_pE1exercise 1
SA209785MM004_1_pE1exercise 1
SA209786MM027_3_pE1exercise 3
SA209787MM036_3_pE1exercise 3
SA209788MM022_3_pE1exercise 3
SA209789MM014_3_pE1exercise 3
SA209790MM026_3_pE1exercise 3
SA209791MM011_3_pE1exercise 3
SA209792MM004_3_pE1exercise 3
SA209793MM035_3_pE1exercise 3
SA209794MM003_3_pE1exercise 3
SA209795MM008_3_pE1exercise 3
SA209796MM010_3_pE1exercise 3
SA209698QC_HP_itMS2_CE0_it08MS2 MS2
SA209699QC_HP_itMS2_CE0_it07MS2 MS2
SA209700QC_HP_itMS2_CE0_it06MS2 MS2
SA209701QC_HP_itMS2_CE10_it01MS2 MS2
SA209702QC_HP_itMS2_CE10_it02MS2 MS2
SA209703QC_HP_itMS2_CE10_it04MS2 MS2
SA209704QC_HP_itMS2_CE10_it03MS2 MS2
SA209705QC_HP_itMS2_CE0_it05MS2 MS2
SA209706QC_HP_itMS2_CE0_it04MS2 MS2
SA209707QC_HP_itMS2_CE40_it06MS2 MS2
SA209708QC_HP_itMS2_CE40_it04MS2 MS2
SA209709QC_HP_itMS2_CE40_it08MS2 MS2
SA209710QC_HP_itMS2_CE40_it05MS2 MS2
SA209711QC_HP_itMS2_CE0_it01MS2 MS2
SA209712QC_HP_itMS2_CE0_it03MS2 MS2
SA209713QC_HP_itMS2_CE0_it02MS2 MS2
SA209714QC_HP_itMS2_CE10_it05MS2 MS2
SA209715QC_HP_itMS2_CE40_it07MS2 MS2
SA209716QC_HP_itMS2_CE20_it06MS2 MS2
SA209717QC_HP_itMS2_CE20_it05MS2 MS2
SA209718QC_HP_itMS2_CE20_it04MS2 MS2
SA209719QC_HP_itMS2_CE20_it07MS2 MS2
SA209720QC_HP_itMS2_CE20_it08MS2 MS2
SA209721QC_HP_itMS2_CE40_it02MS2 MS2
SA209722QC_HP_itMS2_CE40_it01MS2 MS2
SA209723QC_HP_itMS2_CE20_it03MS2 MS2
SA209724QC_HP_itMS2_CE40_it03MS2 MS2
SA209725QC_HP_itMS2_CE10_it07MS2 MS2
SA209726QC_HP_itMS2_CE10_it06MS2 MS2
SA209727QC_HP_itMS2_CE20_it01MS2 MS2
SA209728QC_HP_itMS2_CE10_it08MS2 MS2
SA209729QC_HP_itMS2_CE20_it02MS2 MS2
SA209730QC_HP_10QC QC
SA209731QC_HP_07QC QC
SA209732QC_HP_08QC QC
SA209733QC_HP_09QC QC
SA209734QC_HP_06QC QC
SA209735QC_HP_04QC QC
SA209736QC_HP_01QC QC
SA209737QC_HP_02QC QC
SA209738QC_HP_03QC QC
SA209739QC_HP_11QC QC
SA209740QC_HP_05QC QC
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Collection:

Collection ID:CO002262
Collection Summary:Fasted plasma samples were collected from participants at multiple time points as depicted in Figure 1, taken from the protocol paper Nicol, J.L.;Woodrow, C.;Cunningham, B.J.; Mollee, P.;Weber, N.; Smith, M.D.; Nicol, A.J.; Gordon, L.G.; Hill, M.M.; Skinner, T.L. An Individualized Exercise Intervention for People with Multiple Myeloma—Study Protocol of a Randomized Waitlist-Controlled Trial. Curr. Oncol. 2022, 29, 901–923. https://doi.org/10.3390/curroncol29020077. After overnight fasting, plasma was collected by an experienced phlebotomist from an antecubital vein using a 23-gauge needle into EDTA-coated blood collection tubes and immediately stored on ice. Aliquots were prepared in Eppendorf tubes within 4 hours, and frozen at -80oC until use
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002281
Treatment Summary:Multiple myeloma patients were randomized to exercise (EX) or waitlist (WT) groups as detailed in the protocol paper: Nicol, J.L.;Woodrow, C.;Cunningham, B.J.; Mollee, P.;Weber, N.; Smith, M.D.; Nicol, A.J.; Gordon, L.G.; Hill, M.M.; Skinner, T.L. An Individualized Exercise Intervention for People with Multiple Myeloma—Study Protocol of a Randomized Waitlist-Controlled Trial. Curr. Oncol. 2022, 29, 901–923. https://doi.org/10.3390/curroncol29020077. The individualized exercise program was for 3 months, and follow-up plasma was collected at 12 months. WT group had usual care for 3 months prior to the same exercise and follow-up regime

Sample Preparation:

Sampleprep ID:SP002275
Sampleprep Summary:In total, 126 human plasma samples from 46 patients were prepared. All samples (including QCs and blanks) were randomized in one batch and then evenly split between two 2 mL 96-deepwell plates (Eppendorf #0030 501.306). Human plasma samples were thawed on ice and briefly vortexed before aliquoting 100 µL plasma of each sample to a well. In addition, a global sample pool containing equal volumes (12 µL) of each sample was prepared into a 2 mL Eppendorf tube as quality control (QC) and 12 x 100 µL aliquots were transferred into wells across the 2 plates. Finally, blank negative control extraction samples were prepared by transferring 100 µL of 1X PBS to 6 wells equally across 2 plates. Ten-times the sample volume of ice-cold butanol/methanol (1:1) containing 50 µg/mL antioxidant 2,6-di-tert-butyl-4-methylphenol (BHT) and 0.5 µg/mL ISTD 4-chloro-L-phenylalanine (PCPA) was added to each well using a multi-channel pipette. Plates were covered with organic solvent resistant sealing mats (Eppendorf #0030 127.960) and vortexed for 3 min at 1000 rpm. Samples were then sonicated for 15 min in an ice-cold water bath sonicator, stored overnight at -30oC and centrifuged for 30 min at 4,000 x g (4oC). Samples were aliquoted into 96-well V-bottom plates (Greiner #651201) using a liquid handler platform (AssayMap Bravo, Agilent). From each deepwell plate, 4 x 100 µL and 2 x 200 µL aliquots were prepared, totalling 8 and 4 plates, respectively. Samples were dried down (2.5 hrs) using a Genevac EZ-2 vacuum concentrator and fast-stack swings facilitating drying of 8 plates per batch. Dried sample plates were covered with AlumaSeal CS sealing film for cold storage (Finneran-Porviar #FC-100) and stored at -80oC until LC/MS analysis

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

Chromatography:

Chromatography ID:CH002643
Chromatography Summary:Reversed-phase separation of metabolites was adapted from Evans et al. (2014) with modifications. Separation was achieved on a Zorbax Eclipse Plus C18 RRHD (1.8 μm, 95 Å, 2.1x50mm, #959757-902, Agilent) column held at 40°C and the MS was operated in positive ionization mode. Eluent A was milliQ water and eluent B was methanol both containing 0.1% formic acid. Total method runtime was 8.5 min with the following gradient: 0 min (0.5% eluent B) – 4 min (70% B) – 4.5 min (98% B) – 5.4 min (98% B) – 5.5 min (0.5% B) – 8.5 min (0.5% B). The flow was diverted to waste after 5 minutes and a flow rate of 0.4 mL/min was applied
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1 mm,1.8 µm
Column Temperature:40
Flow Gradient:0 min (0.5% eluent B) - 4 min (70% B) - 4.5 min (98% B) - 5.4 min (98% B) - 5.5 min (0.5% B) - 8.5 min (0.5% B). The flow was diverted to waste after 5 minutes
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH002644
Chromatography Summary:HILIC separation of metabolites was carried out on a Poroshell 120 HILIC-Z (100Å, 2.7µm, 2.1x100mm, #675775-924, Agilent) column at 30ºC and the MS was operated in negative ionization mode. Eluent A was 10 mM ammonium acetate and 5 μM medronic acid in ACN/milliQ 90:10 (pH 9) and eluent B was 10 mM ammonium acetate and 5 μM medronic acid in milliQ (pH 9). Gradient applied was: 0 min (10% eluent B) – 3.5 min (25% B) – 5.5 min (50% B) – 7.5 min (50% B) – 7.6 min (10% B) – 14 min (10% B). Flow rate was set to 0.25 mL/min with a flow ramp to 0.5 mL/min during equilibration
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent Poroshell 120 HILIC-Z (100 2.1mm,2.7um)
Flow Gradient:Gradient applied was: 0 min (10% eluent B) - 3.5 min (25% B) - 5.5 min (50% B) - 7.5 min (50% B) - 7.6 min (10% B) - 14 min (10% B).
Flow Rate:0.25 mL/min
Solvent A:90% acetonitrile/10% water; 10 mM ammonium acetate; 5 µM medronic acid, pH 9
Solvent B:100% water; 10 mM ammonium acetate; 5 µM medronic acid, pH 9
Chromatography Type:HILIC

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
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