Summary of Study ST002996

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 PR001866. The data can be accessed directly via it's Project DOI: 10.21228/M8HM8S 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 IDST002996
Study TitleTissue Lipidomic Profiling for Detection of Non-Small Cell Lung Cancer
Study SummaryUPLC-HRMS analysis was performed on AC and SCC patients. OPLSDA classfication was performed on tumor vs. ANT and 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 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
OUC
DepartmentDepartment of Medicine and Pharmacy
LaboratoryAnalytical chemistry
Last NameZhang
First NameJie
AddressNo. 5 Yushan Road, Qingdao, Shandong, China
Emailzhangjieqau@163.com
Phone17806277823
Submit Date2023-11-16
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-12-27
Release Version1
Jie Zhang Jie Zhang
https://dx.doi.org/10.21228/M8HM8S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001866
Project DOI:doi: 10.21228/M8HM8S
Project Title:Tissue Lipidomic Profiling for Detection of Non-Small Cell Lung Cancer
Project Type:non-targeted lipidomics analysis
Project Summary:NSCLC is the most prevalent type of lung cancer with high mortality rates. In this study, we performed nontargeted lipidomic profiling study of 230 tissue samples from 79 NSCLC patients with adenocarcinoma (AC) or squamous cell carcinoma (SCC) using UPLC-HRMS. oPLS-DA classification models enabled discrimination of tumor from adjacent noncancerous tissue (ANT) and distant noncancerous tissue (DNT) samples in NSCLC and AC with good accuracies (94.1 and 92.0%), sensitivities (93.8 and 91.1%), and specificities (94.2 and 92.5%) using 7 and 8 discriminant compounds, respectively. The discriminant feature panels were verified by external validation sets, revealing characteristic lipid signatures associated with NSCLC and showing prospects for entering the next evaluation stage of biomarker discovery for NSCLC detection and subtyping.
Institute:OUC
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:OUC
Project Comments:OUC
Publications:OUC
Contributors:OUC

Subject:

Subject ID:SU003109
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
SA326177342ade_normadenorm
SA326178336ade_normadenorm
SA326179345ade_normadenorm
SA326180351ade_normadenorm
SA326181357ade_normadenorm
SA326182333ade_normadenorm
SA326183348ade_normadenorm
SA326184315ade_normadenorm
SA326185301ade_normadenorm
SA326186298ade_normadenorm
SA326187304ade_normadenorm
SA326188307ade_normadenorm
SA326189359ade_normadenorm
SA326190312ade_normadenorm
SA326191330ade_normadenorm
SA326192362ade_normadenorm
SA32619319ade_normadenorm
SA32619422ade_normadenorm
SA3261951ade_normadenorm
SA3261964ade_normadenorm
SA326197138ade_normadenorm
SA32619816ade_normadenorm
SA32619910ade_normadenorm
SA3262007ade_normadenorm
SA326201374ade_normadenorm
SA326202365ade_normadenorm
SA326203379ade_normadenorm
SA32620425ade_normadenorm
SA32620513ade_normadenorm
SA326206292ade_normadenorm
SA326207354ade_normadenorm
SA326208194ade_normadenorm
SA326209188ade_normadenorm
SA326210176ade_normadenorm
SA326211200ade_normadenorm
SA326212203ade_normadenorm
SA326213215ade_normadenorm
SA326214206ade_normadenorm
SA326215173ade_normadenorm
SA326216164ade_normadenorm
SA326217286ade_normadenorm
SA326218143ade_normadenorm
SA326219152ade_normadenorm
SA326220155ade_normadenorm
SA326221161ade_normadenorm
SA326222158ade_normadenorm
SA326223218ade_normadenorm
SA326224146ade_normadenorm
SA326225271ade_normadenorm
SA326226221ade_normadenorm
SA326227274ade_normadenorm
SA326228277ade_normadenorm
SA326229283ade_normadenorm
SA326230280ade_normadenorm
SA326231247ade_normadenorm
SA326232259ade_normadenorm
SA326233230ade_normadenorm
SA326234244ade_normadenorm
SA326235232ade_normadenorm
SA326236227ade_normadenorm
SA326237235ade_normadenorm
SA326238241ade_normadenorm
SA326239369ade_sideadeside
SA326240352ade_sideadeside
SA326241355ade_sideadeside
SA326242363ade_sideadeside
SA326243366ade_sideadeside
SA326244360ade_sideadeside
SA326245310ade_sideadeside
SA326246313ade_sideadeside
SA326247375ade_sideadeside
SA326248308ade_sideadeside
SA326249331ade_sideadeside
SA326250337ade_sideadeside
SA326251346ade_sideadeside
SA326252343ade_sideadeside
SA326253349ade_sideadeside
SA32625417ade_sideadeside
SA326255278ade_sideadeside
SA326256228ade_sideadeside
SA326257316ade_sideadeside
SA326258334ade_sideadeside
SA326259305ade_sideadeside
SA3262605ade_sideadeside
SA32626123ade_sideadeside
SA32626226ade_sideadeside
SA32626314ade_sideadeside
SA326264380ade_sideadeside
SA32626520ade_sideadeside
SA32626611ade_sideadeside
SA3262672ade_sideadeside
SA326268377ade_sideadeside
SA3262698ade_sideadeside
SA326270189ade_sideadeside
SA326271177ade_sideadeside
SA326272174ade_sideadeside
SA326273195ade_sideadeside
SA326274201ade_sideadeside
SA326275207ade_sideadeside
SA326276204ade_sideadeside
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Collection:

Collection ID:CO003102
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:TR003118
Treatment Summary:No. Only cancer and noncancerous tissues.

Sample Preparation:

Sampleprep ID:SP003115
Sampleprep Summary:Frozen tissue samples were thawed on ice. Each tissue sample was cut into small pieces and accurately weighed.To 100 mg tissue sample, 1 mL precooled 80% methanol was added and 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.

Combined analysis:

Analysis ID AN004921
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290 Infinity
Column Waters ACQUITY UPLC 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:CH003715
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:0.3 mL min-1
Solvent A:acetonitrile/water
Solvent B:2-propanol/acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS004664
Analysis ID:AN004921
Instrument Name:Thermo LTQ XL
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:capillary temperature 300 °C, capillary voltage 20 V, tube lens 35 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 data processing was applied for artefact removal, blank correction, QC -based signal correction and normalization, etc.
Ion Mode:POSITIVE
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