Summary of Study ST003368

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 PR002091. The data can be accessed directly via it's Project DOI: 10.21228/M8B83W 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 IDST003368
Study TitleNon-Invasive Diagnosis of Moyamoya Disease Using Serum Metabolic Fingerprints and Machine Learning
Study SummaryMoyamoya disease (MMD) is a progressive cerebrovascular condition that elevates the risk of intracranial ischemia and hemorrhage. Timely diagnosis and intervention can considerably lower the chances of new stroke occurrences in MMD patients. However, existing diagnostic techniques are both invasive and costly, with few reports on non-invasive diagnosis using MMD biomarkers. To tackle this challenge, we conducted non-targeted metabolomics analysis using LDI-MS on serum from 288 samples (validation cohort: MMD/HC: 115/115; discovery cohort: MMD/HC: 29/29) to identify patients with MMD. We then created a diagnostic model leveraging deep learning algorithms, which demonstrated remarkable accuracy in distinguishing the MMD group from the HC group (AUC = 0.977, 95% CI of 0.945 to 1.000). This method represents a promising new approach for MMD diagnosis. Additionally, our findings may have wider implications for the diagnosis of other neurological disorders.
Institute
Shanghai Jiao Tong University affiliated Renji Hospital
Last NameXu
First NameYudian
AddressShanghai, 200127, P. R. China, Shanghai, Shanghai, 200127, China
Emailxuyd9r@sjtu.edu.cn
Phone19370718762
Submit Date2024-07-14
Analysis Type DetailMALDI
Release Date2024-09-16
Release Version1
Yudian Xu Yudian Xu
https://dx.doi.org/10.21228/M8B83W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002091
Project DOI:doi: 10.21228/M8B83W
Project Title:Non-Invasive Diagnosis of Moyamoya Disease Using Serum Metabolic Fingerprints and Machine Learning
Project Summary:Moyamoya disease (MMD) is a progressive cerebrovascular disorder that raises the risk of intracranial ischemia and hemorrhage. For a non-invasive diagnostic approach to MMD, we used nanoparticle-enhanced laser desorption/ionization mass spectrometry (LDI-MS) to analyze serum metabolic fingerprints (SMFs) in a validation cohort (MMD: 115/HC: 115) and a discovery cohort (MMD: 29/HC: 29).
Institute:Shanghai Jiao Tong University affiliated Renji Hospital
Last Name:Xu
First Name:Yudian
Address:Shanghai, 200127, P. R. China, Shanghai, Shanghai, 200127, China
Email:xuyd9r@sjtu.edu.cn
Phone:19370718762

Subject:

Subject ID:SU003489
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 Sample source Factor
SA366602Discovery_101Serum HC
SA366603Discovery_95Serum HC
SA366604Discovery_96Serum HC
SA366605Discovery_97Serum HC
SA366606Discovery_98Serum HC
SA366607Discovery_99Serum HC
SA366608Discovery_100Serum HC
SA366609Discovery_102Serum HC
SA366610Discovery_93Serum HC
SA366611Discovery_103Serum HC
SA366612Discovery_104Serum HC
SA366613Discovery_105Serum HC
SA366614Discovery_106Serum HC
SA366615Discovery_107Serum HC
SA366616Discovery_108Serum HC
SA366617Discovery_94Serum HC
SA366618Discovery_92Serum HC
SA366619Discovery_110Serum HC
SA366620Discovery_83Serum HC
SA366621Discovery_77Serum HC
SA366622Discovery_78Serum HC
SA366623Discovery_79Serum HC
SA366624Discovery_80Serum HC
SA366625Discovery_81Serum HC
SA366626Discovery_82Serum HC
SA366627Discovery_84Serum HC
SA366628Discovery_91Serum HC
SA366629Discovery_85Serum HC
SA366630Discovery_86Serum HC
SA366631Discovery_87Serum HC
SA366632Discovery_88Serum HC
SA366633Discovery_89Serum HC
SA366634Discovery_90Serum HC
SA366635Discovery_109Serum HC
SA366636Discovery_111Serum HC
SA366637Discovery_75Serum HC
SA366638Validation_22Serum HC
SA366639Validation_16Serum HC
SA366640Validation_17Serum HC
SA366641Validation_18Serum HC
SA366642Validation_19Serum HC
SA366643Validation_20Serum HC
SA366644Validation_21Serum HC
SA366645Validation_23Serum HC
SA366646Validation_14Serum HC
SA366647Validation_24Serum HC
SA366648Validation_25Serum HC
SA366649Validation_26Serum HC
SA366650Validation_27Serum HC
SA366651Validation_28Serum HC
SA366652Validation_29Serum HC
SA366653Validation_15Serum HC
SA366654Validation_13Serum HC
SA366655Discovery_112Serum HC
SA366656Validation_3Serum HC
SA366657Discovery_113Serum HC
SA366658Discovery_114Serum HC
SA366659Discovery_115Serum HC
SA366660Discovery_2Serum HC
SA366661Validation_1Serum HC
SA366662Validation_2Serum HC
SA366663Validation_4Serum HC
SA366664Validation_12Serum HC
SA366665Validation_5Serum HC
SA366666Validation_6Serum HC
SA366667Validation_7Serum HC
SA366668Validation_8Serum HC
SA366669Validation_9Serum HC
SA366670Validation_10Serum HC
SA366671Validation_11Serum HC
SA366672Discovery_76Serum HC
SA366673Discovery_1Serum HC
SA366674Discovery_74Serum HC
SA366675Discovery_29Serum HC
SA366676Discovery_7Serum HC
SA366677Discovery_6Serum HC
SA366678Discovery_5Serum HC
SA366679Discovery_4Serum HC
SA366680Discovery_3Serum HC
SA366681Discovery_32Serum HC
SA366682Discovery_30Serum HC
SA366683Discovery_9Serum HC
SA366684Discovery_31Serum HC
SA366685Discovery_73Serum HC
SA366686Discovery_28Serum HC
SA366687Discovery_33Serum HC
SA366688Discovery_34Serum HC
SA366689Discovery_35Serum HC
SA366690Discovery_8Serum HC
SA366691Discovery_10Serum HC
SA366692Discovery_37Serum HC
SA366693Discovery_20Serum HC
SA366694Discovery_26Serum HC
SA366695Discovery_25Serum HC
SA366696Discovery_24Serum HC
SA366697Discovery_23Serum HC
SA366698Discovery_22Serum HC
SA366699Discovery_21Serum HC
SA366700Discovery_19Serum HC
SA366701Discovery_11Serum HC
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Collection:

Collection ID:CO003482
Collection Summary:All human peripheral venous blood samples were obtained following the protocols approved by the Institutional Review Board at Huashan Hospital. Blood samples were obtained at the same time as regular blood tests after overnight fasting and then centrifuged for 10 minutes (1500g, 4℃). Serum samples were aliquoted in sterile centrifuge tubes and stored at -80℃ storage freezer.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR003498
Treatment Summary:none

Sample Preparation:

Sampleprep ID:SP003496
Sampleprep Summary:At the beginning, all original serum samples were diluted 10 times by 10ul to obtain diluted serum, and both the original serum and the diluted serum were placed at -80℃ for later use. In LDI MS experiments, 1 μL of analyte solution (prepared standard small metabolites or diluted samples) was first spotted on the polished steel plate and dried, followed by depositing 1 μL of nanoparticle suspension or organic matrix solution and dried in air at room temperature.

Combined analysis:

Analysis ID AN005520
Analysis type MS
Chromatography type None (Direct infusion)
Chromatography system none
Column none
MS Type MALDI
MS instrument type TOF
MS instrument name Bruker Autoflex speed TOF/TOF
Ion Mode POSITIVE
Units Relative intensity

Chromatography:

Chromatography ID:CH004196
Instrument Name:none
Column Name:none
Column Temperature:none
Flow Gradient:none
Flow Rate:none
Solvent A:None
Solvent B:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS005245
Analysis ID:AN005520
Instrument Name:Bruker Autoflex speed TOF/TOF
Instrument Type:TOF
MS Type:MALDI
MS Comments:In a typical LDI MS experiment, ferric particles were dispersed in deionized water at a concentration of 1mg mL-1 for use as a matrix. The organic matrices of CHCA and DHB were dissolved in TA30 solution (acetonitrile/0.1% TFA in water, 7/3, v/v) at a concentration of 10 mg/mL. For the detection of the standards, 100nL of analyte solution (each standard listed in the part of chemicals and reagents) with different density (100ng mL-1, 1μg mL-1, 10μg mL-1, 100μg mL-1, 1mg mL-1) was mixed with 100nL of matrix slurry on the plate and dried for LDI MS analysis. For plasma sample detection, the samples were firstly prepared through protein precipitation, centrifugation, and supernatant filtration according to a commonly applied procedure. Then, a volume of 100nL of plasma solution was spotted on the plate and dried in air at room temperature, followed by adding 100nL of matrix slurry and drying for LDI MS analysis. Then, mass spectra were performed on a 5800 Proteomics Analyzer (Applied Biosystems, Framingham, MA, USA) equipped with a Nd:YAG laser (2 kHz, 355 nm). The acquisitions were extracted in positive reflector ion mode employing delayed extraction with a repetition rate of 1,000Hz and an acceleration voltage of 20 kV. The delay time for this experiment was optimized to 250 ns. The 2,000 laser shots per analysis were for all LDI MS experiments. All the original mass spectra data were visualized in DataExplorer (Version 4.5). Only the m/z signals within 100–300Da and with a signal-to-noise ratio over 3 were then acquired without smoothing processes. For pre-processing, we applied a “home-developed” program using Python (version 3.9) to normalize and standardize the mass spectra data after peak extraction and alignment59. And standard molecules for the accurate mass measurement (±0.05Da) of both Na+-adducted and K+-adducted signals were used to perform the mass calibration. The detection limit of standard metabolites (listed in chemicals and reagents’ part) obtained by ferric particle, DHB, and CHCA-assisted LDI MS were calculated as previously reported
Ion Mode:POSITIVE
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