Summary of Study ST003124

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 PR001942. The data can be accessed directly via it's Project DOI: 10.21228/M8PX4X 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 IDST003124
Study TitleSerum metabolites in inherited retinal degenerations
Study SummaryThe diagnosis of inherited retinal degeneration (IRD) is challenging owing to its phenotypic and genotypic complexity. Clinical information is important before a genetic diagnosis is made. Metabolomics studies the entire picture of bioproducts, which are determined using genetic codes and biological reactions. We demonstrated that the common diagnoses of IRD, including retinitis pigmentosa (RP), cone-rod dystrophy (CRD), Stargardt disease (STGD), and Bietti’s crystalline dystrophy (BCD), could be differentiated based on their metabolite heatmaps. Hundreds of metabolites were identified in the volcano plot compared with that of the control group in every IRD except BCD, considered as potential diagnosing markers. The phenotypes of CRD and STGD overlapped but could be differentiated by their metabolomic features with the assistance of a machine learning model with 100% accuracy. Moreover, EYS-, USH2A-associated, and other RP, sharing considerable similar characteristics in clinical findings, could also be diagnosed using the machine learning model with 85.7% accuracy. Further study would be needed to validate the results in the external dataset. By incorporating mass spectrometry and machine learning, a metabolomics-based diagnostic workflow for the clinical and molecular diagnoses of IRD was proposed in our study.
Institute
National Taiwan University
DepartmentDepartment of Chemistry
LaboratoryCheng-Chih Hsu's lab
Last NameChung
First NameHsin-Hsiang
AddressNo. 1, Sec. 4, Roosevelt Rd.
Emailhhchung@ntu.edu.tw
Phone+886-2-3366-1681
Submit Date2024-03-11
Total Subjects155
Num Males90
Num Females65
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2024-03-17
Release Version1
Hsin-Hsiang Chung Hsin-Hsiang Chung
https://dx.doi.org/10.21228/M8PX4X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001942
Project DOI:doi: 10.21228/M8PX4X
Project Title:Serum metabolites in inherited retinal degenerations
Project Type:Untargeted meetabolomics analysis
Project Summary:Inherited retinal degeneration (IRD) contains a group of retinopathies characterized by high heterogeneity in phenotypes and a widely variable genetic background. The diagnosis of IRD is challenging owing to its phenotypic and genotypic complexity. Metabolomics, the emerging tool investigating comprehensive small molecule constitution of biological samples, provides instantaneous phenotypic information as metabolites reflect both genetic and environmental factors. In this project, we aimed to discover potential biomarkers and establish a diagnosis model for classifying specific IRDs.
Institute:National Taiwan University
Department:Department of Chemistry
Laboratory:Cheng-Chih Hsu's lab
Last Name:Chung
First Name:Hsin-Hsiang
Address:No. 1, Sec. 4, Roosevelt Rd., Taipei, Taipei, 106, Taiwan
Email:hhchung@ntu.edu.tw
Phone:+886-2-3366-1681

Subject:

Subject ID:SU003241
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 Sample source Disease Causative gene
SA338160B448_MPSerum BCD CYP4V2
SA338161B350_MPSerum BCD CYP4V2
SA338162B468_LPSerum BCD CYP4V2
SA338163B461_MPSerum BCD CYP4V2
SA338164B468_MPSerum BCD CYP4V2
SA338165B236_LNSerum BCD CYP4V2
SA338166B204_LNSerum BCD CYP4V2
SA338167B461_LPSerum BCD CYP4V2
SA338168B448_LPSerum BCD CYP4V2
SA338169B204_LPSerum BCD CYP4V2
SA338170B108_MNSerum BCD CYP4V2
SA338171B236_LPSerum BCD CYP4V2
SA338172B284_LPSerum BCD CYP4V2
SA338173B350_LPSerum BCD CYP4V2
SA338174B327_LPSerum BCD CYP4V2
SA338175B284_LNSerum BCD CYP4V2
SA338176B327_LNSerum BCD CYP4V2
SA338177B204_MNSerum BCD CYP4V2
SA338178B236_MNSerum BCD CYP4V2
SA338179B193_MNSerum BCD CYP4V2
SA338180B189_MNSerum BCD CYP4V2
SA338181B143_MNSerum BCD CYP4V2
SA338182B174_MNSerum BCD CYP4V2
SA338183B284_MNSerum BCD CYP4V2
SA338184B051_MNSerum BCD CYP4V2
SA338185B448_LNSerum BCD CYP4V2
SA338186B350_LNSerum BCD CYP4V2
SA338187B461_LNSerum BCD CYP4V2
SA338188B468_LNSerum BCD CYP4V2
SA338189B021_MNSerum BCD CYP4V2
SA338190B002_MNSerum BCD CYP4V2
SA338191B189_LPSerum BCD CYP4V2
SA338192B193_LPSerum BCD CYP4V2
SA338193B021_MPSerum BCD CYP4V2
SA338194B002_MPSerum BCD CYP4V2
SA338195B051_MPSerum BCD CYP4V2
SA338196B108_MPSerum BCD CYP4V2
SA338197B174_MPSerum BCD CYP4V2
SA338198B174_LPSerum BCD CYP4V2
SA338199B193_LNSerum BCD CYP4V2
SA338200B189_LNSerum BCD CYP4V2
SA338201B021_LNSerum BCD CYP4V2
SA338202B002_LNSerum BCD CYP4V2
SA338203B051_LNSerum BCD CYP4V2
SA338204B108_LNSerum BCD CYP4V2
SA338205B174_LNSerum BCD CYP4V2
SA338206B143_LNSerum BCD CYP4V2
SA338207B189_MPSerum BCD CYP4V2
SA338208B143_MPSerum BCD CYP4V2
SA338209B021_LPSerum BCD CYP4V2
SA338210B193_MPSerum BCD CYP4V2
SA338211B051_LPSerum BCD CYP4V2
SA338212B461_MNSerum BCD CYP4V2
SA338213B448_MNSerum BCD CYP4V2
SA338214B327_MNSerum BCD CYP4V2
SA338215B350_MNSerum BCD CYP4V2
SA338216B108_LPSerum BCD CYP4V2
SA338217B143_LPSerum BCD CYP4V2
SA338218B236_MPSerum BCD CYP4V2
SA338219B204_MPSerum BCD CYP4V2
SA338220B284_MPSerum BCD CYP4V2
SA338221B327_MPSerum BCD CYP4V2
SA338222B002_LPSerum BCD CYP4V2
SA338223B468_MNSerum BCD CYP4V2
SA338224C220_LNSerum CDCRD -
SA338225C424_MPSerum CDCRD -
SA338226C121_LNSerum CDCRD -
SA338227C273_LNSerum CDCRD -
SA338228C457_MPSerum CDCRD -
SA338229C442_MPSerum CDCRD -
SA338230C416_MPSerum CDCRD -
SA338231C007_MPSerum CDCRD -
SA338232C285_LNSerum CDCRD -
SA338233C319_LNSerum CDCRD -
SA338234C005_MPSerum CDCRD -
SA338235C168_LNSerum CDCRD -
SA338236C008_MPSerum CDCRD -
SA338237C371_LNSerum CDCRD -
SA338238C375_LNSerum CDCRD -
SA338239C442_LNSerum CDCRD -
SA338240C457_LNSerum CDCRD -
SA338241C424_LNSerum CDCRD -
SA338242C416_LNSerum CDCRD -
SA338243C400_LNSerum CDCRD -
SA338244C012_MPSerum CDCRD -
SA338245C030_MPSerum CDCRD -
SA338246C285_MPSerum CDCRD -
SA338247C273_MPSerum CDCRD -
SA338248C319_MPSerum CDCRD -
SA338249C371_MPSerum CDCRD -
SA338250C375_MPSerum CDCRD -
SA338251C220_MPSerum CDCRD -
SA338252C168_MPSerum CDCRD -
SA338253C120_MPSerum CDCRD -
SA338254C121_MPSerum CDCRD -
SA338255C133_MPSerum CDCRD -
SA338256C144_MPSerum CDCRD -
SA338257C400_MPSerum CDCRD -
SA338258C008_LNSerum CDCRD -
SA338259C030_MNSerum CDCRD -
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Collection:

Collection ID:CO003234
Collection Summary:Patients diagnosed with IRDs, including RP, STGD, CD/CRD, and BCD, at the National Taiwan University Hospital (NTUH) between 2015 and 2020 were prospectively enrolled in this cross-sectional observational study. The study protocol adhered to the tenets of the Declaration of Helsinki and was approved by the Institutional Review Board of NTUH. Serum samples of all participants were collected within 1 to 3 p.m. without fasting status. The serum samples were stored under -80°C before analysis.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR003250
Treatment Summary:Not applicable

Sample Preparation:

Sampleprep ID:SP003248
Sampleprep Summary:The MTBE extraction protocol, with laboratory modifications, was used to extract lipids and polar metabolites from the serum. The 10 μL internal standards (IS) mixture contains 15:0-18:1-d7-PC (2 ppm), 15:0-18:1-d7-PG (2 ppm), and L-tryptophan-(indole-d5) (10 ppm) were spiked into an aliquot of 50 μL serum. Then the sample was extracted by adding 600 μL MTBE and 150 μL MeOH and vortexed for 30 min at room temperature. Next, the sample was added with 200 μL water and centrifuged for 3 min at 13,697 g for phase separation. The upper portion containing serum lipids was transferred to another tube. The extraction was repeated by adding 100 μL water, 100 μL MeOH, and 300 μL MTBE. The sample was vortexed for an additional 10 min and centrifuged for 3 min at 13,697 g. The upper portion was mixed with the lower portion, and the combined solution was dried in a vacuum concentrator (Vacufuge plus Vacuum Concentrator, Eppendorf) for 3 h. The sample reconstitution was performed by adding 100 μL of reconstituted solution (ACN/IPA/water, v/v/v = 65/30/5). For the lower portion, 150 μL cold MeOH was added and stored under a -20°C environment for 2 h, followed by 10 min of 21,401 g centrifugation for protein precipitation. Next, the supernatant was dried using a vacuum concentrator overnight and then reconstituted by adding 100 μL reconstituted solution (ACN/water, v/v = 50/50). The protein precipitation was repeated by mixing 60 μL reconstituted sample with 120 μL cold ACN and then putting the mixtures in a -20°C freezer for an hour. After a 15 min centrifugation at 21,401 g under 4°C, super supernatants (120 μL) were collected and stored under -80°C before further analysis.

Combined analysis:

Analysis ID AN005119 AN005120 AN005121 AN005122
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Peak area Peak area Peak area Peak area

Chromatography:

Chromatography ID:CH003873
Chromatography Summary:Chromatography methods for lipid extract, positive-ion mode.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:50℃
Flow Gradient:0–1 min, 15% B; 1–15 min, 15–70% B; 15-16 min, 70–99% B; 16–18.5 min, 99% B; 18.5–19 min, 99–15% B; and 19-–21 min, 15% B
Flow Rate:0.2 mL/min
Solvent A:Acetonitrile/water (4/6); 0.1% formic acid
Solvent B:Isopropyl alcohol/acetonitrile (9/1); 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH003874
Chromatography Summary:Chromatography methods for lipid extract, negative-ion mode.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:50℃
Flow Gradient:0–0.5 min, 15% B; 0.5–4 min, 15–70% B; 4–15 min, 70–99% B; 15–16.5 min, 99% B; 16.15–17 min, 99–15% B; and 17–19 min, 15% B
Flow Rate:0.2 mL/min
Solvent A:Acetonitrile/water (4/6); 5 mM ammonium acetate
Solvent B:Isopropyl alcohol/acetonitrile (9/1); 5 mM ammonium acetate
Chromatography Type:Reversed phase
  
Chromatography ID:CH003875
Chromatography Summary:Chromatography methods for metabolite extract, positive-ion mode.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:40℃
Flow Gradient:0–1 min, 90% B; 1–9 min, 90-40% B; 9–11.5 min, 40% B; 11.5–12 min, 40–90% B; and 12–14 min, 90% B
Flow Rate:0.25 mL/min
Solvent A:100% Water; 0.1% formic acid
Solvent B:100% Acetonitrile; 0.1% formic acid
Chromatography Type:HILIC
  
Chromatography ID:CH003876
Chromatography Summary:Chromatography methods for metabolite extract, negative-ion mode.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:40℃
Flow Gradient:0–1 min, 90% B; 1–9 min, 90-40% B; 9–11.5 min, 40% B; 11.5–12 min, 40–90% B; and 12–14 min, 90% B
Flow Rate:0.25 mL/min
Solvent A:100% Water; 5 mM ammonium acetate
Solvent B:100% Acetonitrile; 5 mM ammonium acetate
Chromatography Type:HILIC

MS:

MS ID:MS004855
Analysis ID:AN005119
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS data were processed using Thermo Scientific Compound Discoverer v3.2 software.
Ion Mode:POSITIVE
Capillary Temperature:280℃
Ion Source Temperature:180℃
Ion Spray Voltage:3.5 kV
  
MS ID:MS004856
Analysis ID:AN005120
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS data were processed using Thermo Scientific Compound Discoverer v3.2 software.
Ion Mode:NEGATIVE
Capillary Temperature:280℃
Ion Source Temperature:180℃
Ion Spray Voltage:-3.5 kV
  
MS ID:MS004857
Analysis ID:AN005121
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS data were processed using Thermo Scientific Compound Discoverer v3.2 software.
Ion Mode:POSITIVE
Capillary Temperature:280℃
Ion Source Temperature:180℃
Ion Spray Voltage:3.5 kV
  
MS ID:MS004858
Analysis ID:AN005122
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS data were processed using Thermo Scientific Compound Discoverer v3.2 software.
Ion Mode:NEGATIVE
Capillary Temperature:280℃
Ion Source Temperature:180℃
Ion Spray Voltage:-3.5 kV
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