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 ID	ST003124
Study Title	Serum metabolites in inherited retinal degenerations
Study Summary	The 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
Department	Department of Chemistry
Laboratory	Cheng-Chih Hsu's lab
Last Name	Chung
First Name	Hsin-Hsiang
Address	No. 1, Sec. 4, Roosevelt Rd.
Email	hhchung@ntu.edu.tw
Phone	+886-2-3366-1681
Submit Date	2024-03-11
Total Subjects	155
Num Males	90
Num Females	65
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2024-03-17
Release Version	1

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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.

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.