Summary of Study ST003159

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 PR001964. The data can be accessed directly via it's Project DOI: 10.21228/M8VD96 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 IDST003159
Study TitleUntargeted serum metabolomics in the Parkinson's Environment and Genes (PEG) Study
Study SummaryThis project aims to evaluate the serum metabolome of Parkinson’s disease (PD) patients relative to unaffected controls in the Parkinson’s Environment and Genes (PEG) Study. Background: Untargeted high-resolution metabolomic profiling provides simultaneous measurement of thousands of metabolites. Metabolic networks based on these data can help uncover disease-related perturbations across interconnected pathways. Objective: Identify metabolic disturbances associated with PD in the PEG population-based study using untargeted metabolomics. Methods: We provide serum-based untargeted metabolomics data derived from liquid chromatography with high-resolution mass spectrometry (LC-HRMS). LC-HRMS detected 4,762 metabolites for analysis (HILIC: 2716 metabolites; C18: 2046 metabolites).
Institute
University of California, Los Angeles
DepartmentNeurology
Last NamePaul
First NameKimberly
Address710 Westwood Plaza, Los Angeles, CA, 90095, USA
Emailkimberlp@ucla.edu
Phone310.206.7458
Submit Date2023-12-15
Total Subjects919
Analysis Type DetailLC-MS
Release Date2024-04-23
Release Version1
Kimberly Paul Kimberly Paul
https://dx.doi.org/10.21228/M8VD96
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001964
Project DOI:doi: 10.21228/M8VD96
Project Title:Untargeted serum metabolomics in the Parkinson's Environment and Genes (PEG) Study
Project Summary:This project aims to evaluate the serum metabolome of Parkinson’s disease (PD) patients relative to unaffected controls in the Parkinson’s Environment and Genes (PEG) Study. Background: Untargeted high-resolution metabolomic profiling provides simultaneous measurement of thousands of metabolites. Metabolic networks based on these data can help uncover disease-related perturbations across interconnected pathways. Objective: Identify metabolic disturbances associated with PD in the PEG population-based study using untargeted metabolomics. Methods: We provide serum-based untargeted metabolomics data derived from liquid chromatography with high-resolution mass spectrometry (LC-HRMS). LC-HRMS detected 4,762 metabolites for analysis (HILIC: 2716 metabolites; C18: 2046 metabolites).
Institute:University of California Los Angeles
Last Name:Paul
First Name:Kimberly
Address:710 Westwood Plaza, Los Angeles, CA, 90095, USA
Email:kimberlp@ucla.edu
Phone:310.206.7458
Funding Source:National Institute of Environmental Health Sciences
Publications:Paul, K. C., Zhang, K., Walker, D. I., Sinsheimer, J., Yu, Y., Kusters, C., ... & Ritz, B. (2023). Untargeted serum metabolomics reveals novel metabolite associations and disruptions in amino acid and lipid metabolism in Parkinson’s disease. Molecular Neurodegeneration, 18(1), 100.
Contributors:Beate Ritz MD PhD, Dean P. Jones PhD, Kimberly C. Paul PhD, Jeff Bronstein PhD MD

Subject:

Subject ID:SU003277
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Factor Sample source
SA341637VT_190707_M394_236Control Serum
SA341638VT_190707_M394_230Control Serum
SA341639VT_190707_M394_224Control Serum
SA341640VT_200803_M394_092Control Serum
SA341641VT_190707_M394_254Control Serum
SA341642VT_190713_M394_104Control Serum
SA341643VT_190707_M394_260Control Serum
SA341644VT_190713_M394_122Control Serum
SA341645VT_190707_M394_248Control Serum
SA341646VT_190707_M394_200Control Serum
SA341647VT_190707_M394_164Control Serum
SA341648VT_190713_M394_152Control Serum
SA341649VT_190707_M394_146Control Serum
SA341650VT_190707_M394_170Control Serum
SA341651VT_190707_M394_182Control Serum
SA341652VT_200803_M394_116Control Serum
SA341653VT_190707_M394_194Control Serum
SA341654VT_190707_M394_188Control Serum
SA341655VT_190707_M394_206Control Serum
SA341656VT_190708_M394_038Control Serum
SA341657VT_200810_M394_242Control Serum
SA341658VT_200810_M394_248Control Serum
SA341659VT_190708_M394_128Control Serum
SA341660VT_190708_M394_158Control Serum
SA341661VT_190708_M394_164Control Serum
SA341662VT_190713_M394_014Control Serum
SA341663VT_200803_M394_218Control Serum
SA341664VT_190708_M394_170Control Serum
SA341665VT_190708_M394_116Control Serum
SA341666VT_190713_M394_044Control Serum
SA341667VT_200811_M394_086Control Serum
SA341668VT_190708_M394_050Control Serum
SA341669VT_190708_M394_044Control Serum
SA341670VT_200811_M394_044Control Serum
SA341671VT_200803_M394_170Control Serum
SA341672VT_200803_M394_200Control Serum
SA341673VT_190708_M394_098Control Serum
SA341674VT_190707_M394_128Control Serum
SA341675VT_190707_M394_116Control Serum
SA341676VT_190706_M394_176Control Serum
SA341677VT_190713_M394_242Control Serum
SA341678VT_190706_M394_158Control Serum
SA341679VT_190706_M394_182Control Serum
SA341680VT_190706_M394_188Control Serum
SA341681VT_190706_M394_206Control Serum
SA341682VT_190711_M394_128Control Serum
SA341683VT_190706_M394_194Control Serum
SA341684VT_190706_M394_152Control Serum
SA341685VT_190706_M394_146Control Serum
SA341686VT_190706_M394_044Control Serum
SA341687VT_190706_M394_032Control Serum
SA341688VT_190714_M394_080Control Serum
SA341689VT_190706_M394_080Control Serum
SA341690VT_190706_M394_092Control Serum
SA341691VT_200812_M394_218Control Serum
SA341692VT_200812_M394_224Control Serum
SA341693VT_190706_M394_098Control Serum
SA341694VT_190706_M394_212Control Serum
SA341695VT_190713_M394_230Control Serum
SA341696VT_190707_M394_086Control Serum
SA341697VT_190707_M394_080Control Serum
SA341698VT_200802_M394_242Control Serum
SA341699VT_200812_M394_014Control Serum
SA341700VT_190707_M394_098Control Serum
SA341701VT_190708_M394_206Control Serum
SA341702VT_190713_M394_158Control Serum
SA341703VT_190707_M394_104Control Serum
SA341704VT_190713_M394_188Control Serum
SA341705VT_190707_M394_044Control Serum
SA341706VT_200812_M394_116Control Serum
SA341707VT_190706_M394_248Control Serum
SA341708VT_190706_M394_236Control Serum
SA341709VT_190707_M394_014Control Serum
SA341710VT_200802_M394_218Control Serum
SA341711VT_190713_M394_194Control Serum
SA341712VT_190707_M394_032Control Serum
SA341713VT_190707_M394_122Control Serum
SA341714VT_190708_M394_218Control Serum
SA341715VT_190710_M394_176Control Serum
SA341716VT_190712_M394_014Control Serum
SA341717VT_190712_M394_032Control Serum
SA341718VT_190711_M394_260Control Serum
SA341719VT_190710_M394_194Control Serum
SA341720VT_190710_M394_212Control Serum
SA341721VT_200807_M394_146Control Serum
SA341722VT_190710_M394_200Control Serum
SA341723VT_190710_M394_146Control Serum
SA341724VT_190710_M394_128Control Serum
SA341725VT_190710_M394_080Control Serum
SA341726VT_190712_M394_068Control Serum
SA341727VT_190710_M394_056Control Serum
SA341728VT_200805_M394_242Control Serum
SA341729VT_190712_M394_050Control Serum
SA341730VT_190712_M394_038Control Serum
SA341731VT_190710_M394_116Control Serum
SA341732VT_200807_M394_230Control Serum
SA341733VT_190710_M394_218Control Serum
SA341734VT_190711_M394_236Control Serum
SA341735VT_190711_M394_152Control Serum
SA341736VT_190711_M394_164Control Serum
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Collection:

Collection ID:CO003270
Collection Summary:Blood samples were drawn from participants during field visits. Samples were centrifuged, kept on dry ice, and then stored in a −80 °C freezer at UCLA. Serum samples were shipped frozen to Emory University on dry ice for metabolomics analyses, where they were stored at −80 °C until LC-MS processing.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR003286
Treatment Summary:Samples are from participants of the PEG study, which is a population-based Parkinson's disease case-control study from Central California

Sample Preparation:

Sampleprep ID:SP003284
Sampleprep Summary:Blood samples were drawn from participants during field visits. Samples were centrifuged, kept on dry ice, and then stored in a −80 °C freezer at UCLA. Serum samples were shipped frozen to Emory University on dry ice for metabolomics analyses, where they were stored at −80 °C until LC-MS analysis. High-Resolution Metabolomics (HRM) was conducted according to established methods at Emory University (Clincal Biomarkers Laboratory). See the attached SOP protocol. Methods related to the PEG study population and data processing are found in Study_Methods.pdf
Sampleprep Protocol Filename:EmoryUniversity_HRM_SP_082016_01.pdf

Combined analysis:

Analysis ID AN005181 AN005182
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters XBridge BEH Amide (50 x 2.1mm,2.5um) Thermo Higgins C18 (50 x 2.1mm,3um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units log2 transformed intensity log2 transformed intensity

Chromatography:

Chromatography ID:CH003919
Chromatography Summary:The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 microliters of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C.
Methods Filename:EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XBridge BEH Amide (50 x 2.1mm,2.5um)
Column Temperature:60
Flow Gradient:22.5% A, 75% B, 2.5% C hold for 1.5 min, linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min
Flow Rate:0.35 mL/min for 1.5 min; linear increase to 0.4 mL/min at 4 min, hold for 1 mi
Sample Injection:10 uL
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:5 min
Chromatography Type:HILIC
Solvent C:98% water/2% formic acid
  
Chromatography ID:CH003920
Chromatography Summary:The C18 column is operated parallel to the HILIC column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6- port switching valves. During operation of the C18 method, the MS is operated in negative ion mode and 10 μL of sample is injected onto the C18 column while the HILIC column is flushing with wash solution. Flow rate is maintained at 0.4 mL/min until 1.5 min, increased to 0.5 mL/min at 2 min and held for 3 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 10mM ammonium acetate in LC-MS grade water. Initial mmobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min.
Methods Filename:EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Thermo Higgins C18 (50 x 2.1mm,3um)
Column Temperature:60
Flow Gradient:60% A, 35% B, 5% C hold for 0.5 min, linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3 min
Flow Rate:0.4 mL/min for 1.5 min; linear increase to 0.5 mL/min at 2 min held for 3 min
Sample Injection:10 uL
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:5 min
Chromatography Type:Reversed phase
Solvent C:100% water; 10mM ammonium acetate

MS:

MS ID:MS004914
Analysis ID:AN005181
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See attached files
Ion Mode:POSITIVE
Capillary Temperature:250C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:150C
Mass Accuracy:< 3ppm
Spray Voltage:3500
Activation Parameter:5.00E+05
Activation Time:118ms
Interface Voltage:S-Lens RF level= 55
Acquisition Parameters File:EmoryUniversity_HRM_QEHF-MassSpec_092017_v1.pdf
Processing Parameters File:EmoryUniversity_SOP_DataAnalysis_092017_v1.pdf
Analysis Protocol File:Study_Methods.pdf
  
MS ID:MS004915
Analysis ID:AN005182
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See attached files
Ion Mode:NEGATIVE
Capillary Temperature:250C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:150C
Mass Accuracy:< 3ppm
Spray Voltage:-4000
Activation Parameter:5.00E+05
Activation Time:118ms
Interface Voltage:S-Lens RF level= 55
Acquisition Parameters File:EmoryUniversity_HRM_QEHF-MassSpec_092017_v1.pdf
Processing Parameters File:EmoryUniversity_SOP_DataAnalysis_092017_v1.pdf
Analysis Protocol File:Study_Methods.pdf
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