Summary of Study ST002120

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 PR001345. The data can be accessed directly via it's Project DOI: 10.21228/M8VM5R 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 IDST002120
Study TitleFeasibility of detecting AC and SCC using UPLC-HRMS based tissue metabolomics
Study SummaryUPLC-HRMS analysis was performed on AC and SCC patients. OPLSDA classfication was performed on tumor vs. ANT&DNT samples. Panels of discriminant features were identified.The biomarkers 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 shows the abundance of discriminant metabolic features has significant altered in tumor tissues compared to corresponding DNT and ANT samples, indicating metabolic reprogramming during tumorigenesis in AC and SCC.
Institute
Ocean University of China
Last NameZang
First NameXiaoling
AddressNo.5 Yushan Road, Qingdao, Shandong, China
Emailxlingzang@163.com
Phone+86 0532 82032064
Submit Date2022-02-17
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-07-20
Release Version1
Xiaoling Zang Xiaoling Zang
https://dx.doi.org/10.21228/M8VM5R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001345
Project DOI:doi: 10.21228/M8VM5R
Project Title:Non-Small Cell Lung Cancer Detection and Subtyping by UPLC-HRMS Based Tissue Metabolomics
Project Type:non-targeted metabolomics analysis
Project Summary:Non-small cell lung cancer (NSCLC) is the prevalent histological subtype of lung cancer. In this study, we performed ultraperformance liquid chromatography - high resolution mass spectrometry (UPLC-HRMS) based metabolic profiling of 227 tissue samples from 79 lung cancer patients with adenocarcinoma (AC) or squamous cell carcinoma (SCC). oPLS-DA analysis showed detections of AC, SCC and NSCLC were possible with good accuracies (91.3%, 100% and 88.3%), sensitivities (85.7%, 100% and 83.9%), and specificities (94.3%, 100% and 90.7%), respectively. Valine, sphingosine, Glu γ-methyl ester and LPC 16:0 contributed to AC detection and significantly altered in tumor. Valine, sphingosine, LPC 18:1 and leucine derivative contributed to SCC detection. Classification of AC and SCC was also possible (accuracy of 96.8%, sensitivity of 98.2% and specificity of 85.7%) with a panel of 5 metabolites, of which valine and creatine were significantly changed. The classification models were confirmed with external validation sets, showing promise for NSCLC detection and subtyping.
Institute:OUC
Department:Department of Medicine and Pharmacy
Laboratory:Analytical chemistry
Last Name:Zang
First Name:Xiaoling
Address:No. 5 Yushan Road, Qingdao, Shandong, China
Email:zangxiaoling@ouc.edu.cn
Phone:15863037065
Funding Source:OUC
Project Comments:OUC
Publications:OUC
Contributors:OUC

Subject:

Subject ID:SU002205
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
SA204004342ade_normadenorm
SA204005336ade_normadenorm
SA204006345ade_normadenorm
SA204007351ade_normadenorm
SA204008357ade_normadenorm
SA204009333ade_normadenorm
SA204010348ade_normadenorm
SA204011315ade_normadenorm
SA204012301ade_normadenorm
SA204013298ade_normadenorm
SA204014304ade_normadenorm
SA204015307ade_normadenorm
SA204016359ade_normadenorm
SA204017312ade_normadenorm
SA204018330ade_normadenorm
SA204019362ade_normadenorm
SA20402019ade_normadenorm
SA20402122ade_normadenorm
SA2040221ade_normadenorm
SA2040234ade_normadenorm
SA204024138ade_normadenorm
SA20402516ade_normadenorm
SA20402610ade_normadenorm
SA2040277ade_normadenorm
SA204028374ade_normadenorm
SA204029365ade_normadenorm
SA204030379ade_normadenorm
SA20403125ade_normadenorm
SA20403213ade_normadenorm
SA204033292ade_normadenorm
SA204034354ade_normadenorm
SA204035194ade_normadenorm
SA204036188ade_normadenorm
SA204037176ade_normadenorm
SA204038200ade_normadenorm
SA204039203ade_normadenorm
SA204040215ade_normadenorm
SA204041206ade_normadenorm
SA204042173ade_normadenorm
SA204043164ade_normadenorm
SA204044286ade_normadenorm
SA204045143ade_normadenorm
SA204046152ade_normadenorm
SA204047155ade_normadenorm
SA204048161ade_normadenorm
SA204049158ade_normadenorm
SA204050218ade_normadenorm
SA204051146ade_normadenorm
SA204052271ade_normadenorm
SA204053221ade_normadenorm
SA204054274ade_normadenorm
SA204055277ade_normadenorm
SA204056283ade_normadenorm
SA204057280ade_normadenorm
SA204058247ade_normadenorm
SA204059259ade_normadenorm
SA204060230ade_normadenorm
SA204061244ade_normadenorm
SA204062232ade_normadenorm
SA204063227ade_normadenorm
SA204064235ade_normadenorm
SA204065241ade_normadenorm
SA204066355ade_sideadeside
SA204067352ade_sideadeside
SA204068369ade_sideadeside
SA204069363ade_sideadeside
SA204070366ade_sideadeside
SA204071360ade_sideadeside
SA204072310ade_sideadeside
SA204073313ade_sideadeside
SA204074375ade_sideadeside
SA204075308ade_sideadeside
SA204076331ade_sideadeside
SA204077337ade_sideadeside
SA204078346ade_sideadeside
SA204079343ade_sideadeside
SA204080349ade_sideadeside
SA20408117ade_sideadeside
SA204082278ade_sideadeside
SA204083228ade_sideadeside
SA204084316ade_sideadeside
SA204085334ade_sideadeside
SA204086305ade_sideadeside
SA2040875ade_sideadeside
SA20408823ade_sideadeside
SA20408926ade_sideadeside
SA20409014ade_sideadeside
SA204091380ade_sideadeside
SA20409220ade_sideadeside
SA2040938ade_sideadeside
SA2040942ade_sideadeside
SA204095377ade_sideadeside
SA20409611ade_sideadeside
SA204097189ade_sideadeside
SA204098177ade_sideadeside
SA204099174ade_sideadeside
SA204100195ade_sideadeside
SA204101201ade_sideadeside
SA204102207ade_sideadeside
SA204103204ade_sideadeside
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Collection:

Collection ID:CO002198
Collection Summary:The patient tissue specimens from 79 NSCLC patients including the two most prevalent histological subtypes adenocarcinoma (ade) and squamous cell (squ) tumor (65 ade patients with age range 36-84; 14 squ patients with age range 49-78) were obtained from Beijing Hospital. Primary tumor tissues, paired adjacent non-cancerous tissues (ANT) (within 2 cm apart from tumor edge) and distant normal tissues (DNT) ( > 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-206-02) and also approved by the Ocean University of China (OUC-HM-2022-002).
Sample Type:Lung
Collection Method:Surgical resect
Collection Location:Beijing Hospital
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002217
Treatment Summary:No. Only cancer and noncancerous tissues.

Sample Preparation:

Sampleprep ID:SP002211
Sampleprep Summary:Frozen tissue samples were thawed on ice. Each tissue sample was cut into small pieces and accurately weighed. One mL of precooled 80% methanol was added to 100 mg of tissue and the sample mixture was homogenized (60 Hz, 90 seconds). In a tissue homogenizer with precooled module, followed by vortex-mixing for 1 min and incubation at -80 °C for 4 h to allow for sufficient metabolite extraction. Subsequently, the samples were centrifuged at 14,000 × g for 10 min at 4 °C, and the supernatant was collected and dried under vacuum. Sample blanks were prepared using water following the same experimental procedure. Before analysis, dried metabolites were reconstituted with 100 μL LC-MS grade water, vortex-mixed, and centrifuged at 14,000 × g for 10 min to remove insoluble particles prior to UPLC-HRMS analysis. Quality control (QC) samples were prepared by pooling a small volume from samples with enough volume.

Combined analysis:

Analysis ID AN003471
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290 Infinity
Column Waters Acquity BEH C18 (50 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo LTQ XL
Ion Mode POSITIVE
Units Peak Area

Chromatography:

Chromatography ID:CH002562
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH C18 (50 x 2.1mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003232
Analysis ID:AN003471
Instrument Name:Thermo LTQ XL
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:capillary temperature 300 °C, capillary voltage 20 V, tube lens 20 V, spray voltage 4.0 kV for positive ion mode, auxiliary gas, sheath gas and sweep gas flow rate 10, 40, and 0 arbitrary units. Progenesis QI version 2.4 was used for raw data processing. FORTRAN based home-built secondary metabolomics data processing was applied for artefact removal, blank correction, QC -based signal correction and normalization, etc.
Ion Mode:POSITIVE
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