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.
| Study ID | ST003159 |
| Study Title | Untargeted serum metabolomics in the Parkinson's Environment and Genes (PEG) Study |
| Study 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 |
| Department | Neurology |
| Last Name | Paul |
| First Name | Kimberly |
| Address | 710 Westwood Plaza, Los Angeles, CA, 90095, USA |
| kimberlp@ucla.edu | |
| Phone | 310.206.7458 |
| Submit Date | 2023-12-15 |
| Total Subjects | 919 |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-04-23 |
| Release Version | 1 |
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 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor | Sample source |
|---|---|---|---|
| SA341637 | VT_190707_M394_236 | Control | Serum |
| SA341638 | VT_190707_M394_230 | Control | Serum |
| SA341639 | VT_190707_M394_224 | Control | Serum |
| SA341640 | VT_200803_M394_092 | Control | Serum |
| SA341641 | VT_190707_M394_254 | Control | Serum |
| SA341642 | VT_190713_M394_104 | Control | Serum |
| SA341643 | VT_190707_M394_260 | Control | Serum |
| SA341644 | VT_190713_M394_122 | Control | Serum |
| SA341645 | VT_190707_M394_248 | Control | Serum |
| SA341646 | VT_190707_M394_200 | Control | Serum |
| SA341647 | VT_190707_M394_164 | Control | Serum |
| SA341648 | VT_190713_M394_152 | Control | Serum |
| SA341649 | VT_190707_M394_146 | Control | Serum |
| SA341650 | VT_190707_M394_170 | Control | Serum |
| SA341651 | VT_190707_M394_182 | Control | Serum |
| SA341652 | VT_200803_M394_116 | Control | Serum |
| SA341653 | VT_190707_M394_194 | Control | Serum |
| SA341654 | VT_190707_M394_188 | Control | Serum |
| SA341655 | VT_190707_M394_206 | Control | Serum |
| SA341656 | VT_190708_M394_038 | Control | Serum |
| SA341657 | VT_200810_M394_242 | Control | Serum |
| SA341658 | VT_200810_M394_248 | Control | Serum |
| SA341659 | VT_190708_M394_128 | Control | Serum |
| SA341660 | VT_190708_M394_158 | Control | Serum |
| SA341661 | VT_190708_M394_164 | Control | Serum |
| SA341662 | VT_190713_M394_014 | Control | Serum |
| SA341663 | VT_200803_M394_218 | Control | Serum |
| SA341664 | VT_190708_M394_170 | Control | Serum |
| SA341665 | VT_190708_M394_116 | Control | Serum |
| SA341666 | VT_190713_M394_044 | Control | Serum |
| SA341667 | VT_200811_M394_086 | Control | Serum |
| SA341668 | VT_190708_M394_050 | Control | Serum |
| SA341669 | VT_190708_M394_044 | Control | Serum |
| SA341670 | VT_200811_M394_044 | Control | Serum |
| SA341671 | VT_200803_M394_170 | Control | Serum |
| SA341672 | VT_200803_M394_200 | Control | Serum |
| SA341673 | VT_190708_M394_098 | Control | Serum |
| SA341674 | VT_190707_M394_128 | Control | Serum |
| SA341675 | VT_190707_M394_116 | Control | Serum |
| SA341676 | VT_190706_M394_176 | Control | Serum |
| SA341677 | VT_190713_M394_242 | Control | Serum |
| SA341678 | VT_190706_M394_158 | Control | Serum |
| SA341679 | VT_190706_M394_182 | Control | Serum |
| SA341680 | VT_190706_M394_188 | Control | Serum |
| SA341681 | VT_190706_M394_206 | Control | Serum |
| SA341682 | VT_190711_M394_128 | Control | Serum |
| SA341683 | VT_190706_M394_194 | Control | Serum |
| SA341684 | VT_190706_M394_152 | Control | Serum |
| SA341685 | VT_190706_M394_146 | Control | Serum |
| SA341686 | VT_190706_M394_044 | Control | Serum |
| SA341687 | VT_190706_M394_032 | Control | Serum |
| SA341688 | VT_190714_M394_080 | Control | Serum |
| SA341689 | VT_190706_M394_080 | Control | Serum |
| SA341690 | VT_190706_M394_092 | Control | Serum |
| SA341691 | VT_200812_M394_218 | Control | Serum |
| SA341692 | VT_200812_M394_224 | Control | Serum |
| SA341693 | VT_190706_M394_098 | Control | Serum |
| SA341694 | VT_190706_M394_212 | Control | Serum |
| SA341695 | VT_190713_M394_230 | Control | Serum |
| SA341696 | VT_190707_M394_086 | Control | Serum |
| SA341697 | VT_190707_M394_080 | Control | Serum |
| SA341698 | VT_200802_M394_242 | Control | Serum |
| SA341699 | VT_200812_M394_014 | Control | Serum |
| SA341700 | VT_190707_M394_098 | Control | Serum |
| SA341701 | VT_190708_M394_206 | Control | Serum |
| SA341702 | VT_190713_M394_158 | Control | Serum |
| SA341703 | VT_190707_M394_104 | Control | Serum |
| SA341704 | VT_190713_M394_188 | Control | Serum |
| SA341705 | VT_190707_M394_044 | Control | Serum |
| SA341706 | VT_200812_M394_116 | Control | Serum |
| SA341707 | VT_190706_M394_248 | Control | Serum |
| SA341708 | VT_190706_M394_236 | Control | Serum |
| SA341709 | VT_190707_M394_014 | Control | Serum |
| SA341710 | VT_200802_M394_218 | Control | Serum |
| SA341711 | VT_190713_M394_194 | Control | Serum |
| SA341712 | VT_190707_M394_032 | Control | Serum |
| SA341713 | VT_190707_M394_122 | Control | Serum |
| SA341714 | VT_190708_M394_218 | Control | Serum |
| SA341715 | VT_190710_M394_176 | Control | Serum |
| SA341716 | VT_190712_M394_014 | Control | Serum |
| SA341717 | VT_190712_M394_032 | Control | Serum |
| SA341718 | VT_190711_M394_260 | Control | Serum |
| SA341719 | VT_190710_M394_194 | Control | Serum |
| SA341720 | VT_190710_M394_212 | Control | Serum |
| SA341721 | VT_200807_M394_146 | Control | Serum |
| SA341722 | VT_190710_M394_200 | Control | Serum |
| SA341723 | VT_190710_M394_146 | Control | Serum |
| SA341724 | VT_190710_M394_128 | Control | Serum |
| SA341725 | VT_190710_M394_080 | Control | Serum |
| SA341726 | VT_190712_M394_068 | Control | Serum |
| SA341727 | VT_190710_M394_056 | Control | Serum |
| SA341728 | VT_200805_M394_242 | Control | Serum |
| SA341729 | VT_190712_M394_050 | Control | Serum |
| SA341730 | VT_190712_M394_038 | Control | Serum |
| SA341731 | VT_190710_M394_116 | Control | Serum |
| SA341732 | VT_200807_M394_230 | Control | Serum |
| SA341733 | VT_190710_M394_218 | Control | Serum |
| SA341734 | VT_190711_M394_236 | Control | Serum |
| SA341735 | VT_190711_M394_152 | Control | Serum |
| SA341736 | VT_190711_M394_164 | Control | Serum |
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 |
