Summary of Study ST003756

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 PR002340. The data can be accessed directly via it's Project DOI: 10.21228/M85C1M 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 IDST003756
Study TitleUltrahigh-performance liquid chromatography–high-resolution mass spectrometry-based tissue lipidomics study of thymoma and thymic hyperplasia
Study SummaryUPLC-HRMS analysis was performed on thymoma and thymic hyperplasia patients. OPLSDA classfication was performed on tumor vs. ANT and DNT samples. Panels of discriminant compounds were identified. The compounds identified in discovery set samples for each binary classification were confirmed by using a set of validation samples, which were run separately. Additionally, paired analysis showed the abundance of discriminant compounds has significant altered in tumor tissues compared to corresponding DNT and ANT samples, reflecting the lipid characteristics related to tumor in situ and cancer cell signaling.
Institute
Ocean University of China
DepartmentDepartment of Medicine and Pharmacy
LaboratoryAnalytical chemistry
Last NameZhang
First NameJie
AddressNo. 5 Yushan Road, Qingdao, Shandong, China
Emailzhangjieqau@163.com
Phone17806277823
Submit Date2025-02-15
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-08-15
Release Version1
Jie Zhang Jie Zhang
https://dx.doi.org/10.21228/M85C1M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002340
Project DOI:doi: 10.21228/M85C1M
Project Title:Ultrahigh-performance liquid chromatography–high-resolution mass spectrometry-based tissue lipidomics study of thymoma and thymic hyperplasia
Project Type:non-targeted lipidomics analysis
Project Summary:Thymoma is a rare malignant thymic epithelial tumor (TET) with an incidence of about 2 to 4 per million. In this study, we performed nontargeted lipidomic profiling study of tissue samples from 39 patients with thymoma and thymic hyperplasia using UPLC-HRMS. OPLS-DA classification models enabled discrimination of tumor from adjacent noncancerous tissue (ANT) and distant noncancerous tissue (DNT) samples in thymoma with good accuracy, sensitivity, and specificity using 5 discriminant compounds. The discriminant feature panels were verified by external validation sets, revealing characteristic lipid signatures associated with thymoma and showing prospects for entering the next evaluation stage of biomarker discovery for thymoma detection, giving hints to potential treatment targets for the disease.
Institute:Ocean University of China
Department:Department of Medicine and Pharmacy
Laboratory:Analytical chemistry
Last Name:Zhang
First Name:Jie
Address:No. 5 Yushan Road, Qingdao, Shandong, China
Email:zhangjieqau@163.com
Phone:17806277823
Funding Source:ocean university of China

Subject:

Subject ID:SU003889
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 Tissue type Sample source
SA408956114nodu_normnodu_norm thymic hyperplasia
SA40895794str_nodu_normnodu_norm thymic hyperplasia
SA40895876str_nodu_normnodu_norm thymic hyperplasia
SA40895956str_nodu_normnodu_norm thymic hyperplasia
SA40896039nodu_normnodu_norm thymic hyperplasia
SA40896134nodu_normnodu_norm thymic hyperplasia
SA40896284nodu_normnodu_norm thymic hyperplasia
SA40896333nodu_normnodu_norm thymic hyperplasia
SA40896449nodu_normnodu_norm thymic hyperplasia
SA40896555nodu_normnodu_norm thymic hyperplasia
SA40896644nodu_normnodu_norm thymic hyperplasia
SA40896737nodu_normnodu_norm thymic hyperplasia
SA40896896str_nodu_sidenodu_side thymic hyperplasia
SA408969116str_nodu_sidenodu_side thymic hyperplasia
SA40897034nodu_sidenodu_side thymic hyperplasia
SA4089717nodu_sidenodu_side thymic hyperplasia
SA40897211nodu_sidenodu_side thymic hyperplasia
SA408973140nodu_sidenodu_side thymic hyperplasia
SA40897456nodu_sidenodu_side thymic hyperplasia
SA40897551nodu_sidenodu_side thymic hyperplasia
SA40897648nodu_sidenodu_side thymic hyperplasia
SA40897740nodu_sidenodu_side thymic hyperplasia
SA40897835nodu_sidenodu_side thymic hyperplasia
SA40897922nodu_sidenodu_side thymic hyperplasia
SA40898086str_nodu_sidenodu_side thymic hyperplasia
SA4089818nodu_tumornodu_tumor thymic hyperplasia
SA40898235nodu_tumornodu_tumor thymic hyperplasia
SA4089832301nodu_tumornodu_tumor thymic hyperplasia
SA40898436nodu_tumornodu_tumor thymic hyperplasia
SA4089853thymo_normthymo_norm thymoma
SA408986106str_thymo_normthymo_norm thymoma
SA40898728thymo_normthymo_norm thymoma
SA40898823_02thymo_normthymo_norm thymoma
SA40898921thymo_normthymo_norm thymoma
SA40899015_02thymo_normthymo_norm thymoma
SA40899123thymo_normthymo_norm thymoma
SA40899264thymo_normthymo_norm thymoma
SA40899359thymo_normthymo_norm thymoma
SA40899453thymo_normthymo_norm thymoma
SA40899537thymo_normthymo_norm thymoma
SA40899631thymo_normthymo_norm thymoma
SA40899726thymo_normthymo_norm thymoma
SA40899818thymo_normthymo_norm thymoma
SA40899915thymo_normthymo_norm thymoma
SA40900013thymo_normthymo_norm thymoma
SA40900110thymo_normthymo_norm thymoma
SA4090027thymo_normthymo_norm thymoma
SA4090034thymo_normthymo_norm thymoma
SA4090041thymo_normthymo_norm thymoma
SA409005109str_thymo_sidethymo_side thymoma
SA40900620thymo_sidethymo_side thymoma
SA40900711str_thymo_sidethymo_side thymoma
SA40900833thymo_sidethymo_side thymoma
SA40900916_02thymo_sidethymo_side thymoma
SA4090104thymo_sidethymo_side thymoma
SA4090112thymo_sidethymo_side thymoma
SA4090128thymo_sidethymo_side thymoma
SA40901316thymo_sidethymo_side thymoma
SA40901425thymo_sidethymo_side thymoma
SA40901530thymo_sidethymo_side thymoma
SA40901641thymo_sidethymo_side thymoma
SA40901757thymo_sidethymo_side thymoma
SA409018103thymo_sidethymo_side thymoma
SA40901919thymo_sidethymo_side thymoma
SA40902042thymo_tumorthymo_tumor thymoma
SA40902132thymo_tumorthymo_tumor thymoma
SA4090225thymo_tumorthymo_tumor thymoma
SA409023110str_thymo_tumorthymo_tumor thymoma
SA40902414thymo_tumorthymo_tumor thymoma
SA409025108str_thymo_tumorthymo_tumor thymoma
SA40902617thymo_tumorthymo_tumor thymoma
SA40902798str_thymo_tumorthymo_tumor thymoma
SA40902820thymo_tumorthymo_tumor thymoma
SA40902924thymo_tumorthymo_tumor thymoma
SA40903027thymo_tumorthymo_tumor thymoma
SA40903129thymo_tumorthymo_tumor thymoma
SA409032163str_thymo_tumorthymo_tumor thymoma
SA40903343thymo_tumorthymo_tumor thymoma
SA40903438thymo_tumorthymo_tumor thymoma
SA40903544thymo_tumorthymo_tumor thymoma
SA40903624_02thymo_tumorthymo_tumor thymoma
SA40903722thymo_tumorthymo_tumor thymoma
SA4090383thymo_tumorthymo_tumor thymoma
SA4090395_02thymo_tumorthymo_tumor thymoma
SA40904060thymo_tumorthymo_tumor thymoma
SA40904158thymo_tumorthymo_tumor thymoma
SA40904254thymo_tumorthymo_tumor thymoma
SA40904346thymo_tumorthymo_tumor thymoma
SA40904417_02thymo_tumorthymo_tumor thymoma
Showing results 1 to 89 of 89

Collection:

Collection ID:CO003882
Collection Summary:The patient tissue specimens from 39 patients including the two most prevalent histological subtypes thymoma ("thymo") and thymic hyperplasia ("nodu") were obtained from Beijing Hospital. Primary tumor tissues, paired adjacent non-cancerous tissues (ANT or "side") (within 2 cm apart from tumor edge) and distant normal tissues (DNT or "norm")) ( > 2 cm apart from tumor edge) were surgically resected and frozen at −80 °C until metabolite extraction. The study was approved by the Research Ethics Committee of Beijing Hospital (2019BJYYEC-200-02) and also approved by the Ocean University of China (OUC-HM-2022-002). In the tissue type column of the study design, the abbreviated form "nodu" stands for thymic hyperplasia, "norm" stands for DNT, and "side" stands for ANT.
Sample Type:Thymus
Collection Method:Surgical resect
Collection Location:Beijing Hospital
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003898
Treatment Summary:No. Only cancer and noncancerous tissues.

Sample Preparation:

Sampleprep ID:SP003895
Sampleprep Summary:Frozen tissue samples of approximately 10-100 mg were thawed on ice, and 1 mL of precooled 80% methanol was added to 100 mg tissue sample.The sample was homogenized (60 Hz, 90 s) in a tissue homogenizer (Jingxin, JX-24, Shanghai, China). After vortexing for 1 min, the mixture was incubated at -80 °C for 4 hours, followed by centrifuging at 14,000 × g for 10 min at 4 °C. The supernatant was transferred to a new tube. To the rest of the sample, 400 μL dichloromethane/ methanol (3:1, v/v) was added for lipid extraction. The sample mixture was then vortexed twice, each time for 30 s, followed by incubation at -80 °C for 30 min. After homogenization (60 Hz, 90 s) and centrifugation of the sample at 14,000 × g for 10 min at 4 °C, the supernatant was collected and dried under a speed vacuum concentrator.

Chromatography:

Chromatography ID:CH004683
Chromatography Summary:Reversed phase chromatography was employed using a Waters ACQUITY UPLC BEH C18 column (2.1 mm × 50 mm and 1.7 μm particle size; Waters Corporation, Milford, MA). Mobile phase A consisted of water/acetonitrile (40:60, v/v) with 0.1% formic acid and 10 mM ammonium formate, and mobile phase B comprised acetonitrile/2-propanol (10:90, v/v) with 0.1% formic acid and 10 mM ammonium formate.
Instrument Name:Agilent 1290 Infinity
Column Name:Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um)
Column Temperature:50
Flow Gradient:0-2 min, 60%-57% A, 2-2.1 min 57%-50% A, 2.1-12 min 50%-46% A, 12-12.1 min 46%-30% A, 12.1-18 min 30%-1% A
Flow Rate:0.3mL/min
Solvent A:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006167
Analysis Type:MS
Chromatography ID:CH004683
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003756_AN006167_Results.txt
Units:peak area
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