Summary of Study ST003950

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 PR002474. The data can be accessed directly via it's Project DOI: 10.21228/M8V84X 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.

Study ID	ST003950
Study Title	Plasma Phospholipids Analysis in Thai EGFR-mutated Non-Small Cell Lung Cancer Patients
Study Summary	Lung cancer remains the leading cause of cancer-related deaths worldwide, emphasizing an urgent need for effective, non-invasive diagnostic and prognostic biomarkers. Metabolic reprogramming driven by oncogenic driver alterations, especially EGFR mutations in non-small cell lung cancer (NSCLC), provides promising metabolic signatures detectable in plasma. This study aimed to identify plasma metabolomic biomarkers distinguishing healthy individuals from NSCLC patients and to further stratify NSCLC patients by EGFR mutation status and EGFR tyrosine kinase inhibitor (TKI) resistance. Using liquid chromatography-mass spectrometry (LC-MS/MS), we quantified 8 phospholipids of 78 individuals, including NSCLC patients and healthy controls.
Institute	Mahidol University
Last Name	Khoomrung
First Name	Sakda
Address	2 Wanglang road, Bangkoknoi, Bangkok 10700. Thailand.
Email	siriphan.man@mahidol.edu
Phone	025195505
Submit Date	2025-05-28
Raw Data Available	Yes
Raw Data File Type(s)	mzML, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2025-07-07
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002474
Project DOI:	doi: 10.21228/M8V84X
Project Title:	Plasma Metabolomic Analysis in Thai EGFR-mutated Non-Small Cell Lung Cancer Patients
Project Summary:	Lung cancer remains the leading cause of cancer-related deaths worldwide, emphasizing an urgent need for effective, non-invasive diagnostic and prognostic biomarkers. Metabolic reprogramming driven by oncogenic driver alterations, especially EGFR mutations in non-small cell lung cancer (NSCLC), provides promising metabolic signatures detectable in plasma. This study aimed to identify plasma metabolomic biomarkers distinguishing healthy individuals from NSCLC patients and to further stratify NSCLC patients by EGFR mutation status and EGFR tyrosine kinase inhibitor (TKI) resistance. Using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS/MS), we quantified four groups of targeted metabolites (amino acids, organic acids, sugar and sugar alcohols, and phospholipids) of 78 individuals, including NSCLC patients and healthy controls. Metabolomic signatures distinctly separated healthy controls from NSCLC patients and, furthermore, EGFR-mutated NSCLC from EGFR wild-type cases. Additionally, metabolomics results effectively distinguished EGFR TKI-resistant from treatment-naïve EGFR-mutated NSCLC. Our findings highlight the potential of plasma metabolites as minimally invasive biomarkers for molecular classification and monitoring therapeutic response in NSCLC patients.
Institute:	Mahidol University
Last Name:	Khoomrung
First Name:	Sakda
Address:	2 Wanglang road, Bangkoknoi, Bangkok 10700. Thailand.
Email:	Sakda.kho@mahidol.edu
Phone:	024195505

Subject:

Subject ID:	SU004087
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	Disease	EGFR mutation	Treatment
SA452308	C4	Plasma	Healthy	n/a	n/a
SA452309	C1	Plasma	Healthy	n/a	n/a
SA452310	C2	Plasma	Healthy	n/a	n/a
SA452311	C3	Plasma	Healthy	n/a	n/a
SA452312	C10	Plasma	Healthy	n/a	n/a
SA452313	C5	Plasma	Healthy	n/a	n/a
SA452314	C6	Plasma	Healthy	n/a	n/a
SA452315	C7	Plasma	Healthy	n/a	n/a
SA452316	C8	Plasma	Healthy	n/a	n/a
SA452317	C9	Plasma	Healthy	n/a	n/a
SA452318	B27	Plasma	NSCLC	No	Naïve
SA452319	B17	Plasma	NSCLC	No	Naïve
SA452320	B18	Plasma	NSCLC	No	Naïve
SA452321	B2	Plasma	NSCLC	No	Naïve
SA452322	B21	Plasma	NSCLC	No	Naïve
SA452323	B22	Plasma	NSCLC	No	Naïve
SA452324	B23	Plasma	NSCLC	No	Naïve
SA452325	B24	Plasma	NSCLC	No	Naïve
SA452326	B25	Plasma	NSCLC	No	Naïve
SA452327	B26	Plasma	NSCLC	No	Naïve
SA452328	B5	Plasma	NSCLC	No	Naïve
SA452329	B28	Plasma	NSCLC	No	Naïve
SA452330	B30	Plasma	NSCLC	No	Naïve
SA452331	B33	Plasma	NSCLC	No	Naïve
SA452332	B34	Plasma	NSCLC	No	Naïve
SA452333	B42	Plasma	NSCLC	No	Naïve
SA452334	B15	Plasma	NSCLC	No	Naïve
SA452335	B6	Plasma	NSCLC	No	Naïve
SA452336	B7	Plasma	NSCLC	No	Naïve
SA452337	B8	Plasma	NSCLC	No	Naïve
SA452338	B9	Plasma	NSCLC	No	Naïve
SA452339	B16	Plasma	NSCLC	No	Naïve
SA452340	B19	Plasma	NSCLC	No	Naïve
SA452341	B14	Plasma	NSCLC	No	Naïve
SA452342	B12	Plasma	NSCLC	No	Naïve
SA452343	B11	Plasma	NSCLC	No	Naïve
SA452344	B10	Plasma	NSCLC	No	Naïve
SA452345	B13	Plasma	NSCLC	No	Naïve
SA452346	B1	Plasma	NSCLC	No	Naïve
SA452347	A25	Plasma	NSCLC	Yes	Naïve
SA452348	A29	Plasma	NSCLC	Yes	Naïve
SA452349	A28	Plasma	NSCLC	Yes	Naïve
SA452350	A27	Plasma	NSCLC	Yes	Naïve
SA452351	A26	Plasma	NSCLC	Yes	Naïve
SA452352	A22	Plasma	NSCLC	Yes	Naïve
SA452353	A24	Plasma	NSCLC	Yes	Naïve
SA452354	A23	Plasma	NSCLC	Yes	Naïve
SA452355	A32	Plasma	NSCLC	Yes	Naïve
SA452356	A20	Plasma	NSCLC	Yes	Naïve
SA452357	A2	Plasma	NSCLC	Yes	Naïve
SA452358	A14	Plasma	NSCLC	Yes	Naïve
SA452359	A31	Plasma	NSCLC	Yes	Naïve
SA452360	A30	Plasma	NSCLC	Yes	Naïve
SA452361	A33	Plasma	NSCLC	Yes	Naïve
SA452362	A41	Plasma	NSCLC	Yes	Naïve
SA452363	A13	Plasma	NSCLC	Yes	Naïve
SA452364	A34	Plasma	NSCLC	Yes	Naïve
SA452365	A45	Plasma	NSCLC	Yes	Naïve
SA452366	A43	Plasma	NSCLC	Yes	Naïve
SA452367	A42	Plasma	NSCLC	Yes	Naïve
SA452368	A46	Plasma	NSCLC	Yes	Naïve
SA452369	A40	Plasma	NSCLC	Yes	Naïve
SA452370	A35	Plasma	NSCLC	Yes	Naïve
SA452371	A39	Plasma	NSCLC	Yes	Naïve
SA452372	A1	Plasma	NSCLC	Yes	Naïve
SA452373	A36	Plasma	NSCLC	Yes	Naïve
SA452374	A37	Plasma	NSCLC	Yes	Naïve
SA452375	A38	Plasma	NSCLC	Yes	Naïve
SA452376	D1	Plasma	NSCLC	Yes	TKI resistant
SA452377	D10	Plasma	NSCLC	Yes	TKI resistant
SA452378	D2	Plasma	NSCLC	Yes	TKI resistant
SA452379	D3	Plasma	NSCLC	Yes	TKI resistant
SA452380	D4	Plasma	NSCLC	Yes	TKI resistant
SA452381	D5	Plasma	NSCLC	Yes	TKI resistant
SA452382	D6	Plasma	NSCLC	Yes	TKI resistant
SA452383	D8	Plasma	NSCLC	Yes	TKI resistant
SA452384	D9	Plasma	NSCLC	Yes	TKI resistant
SA452385	D11	Plasma	NSCLC	Yes	TKI resistant

Showing results 1 to 78 of 78

Showing results 1 to 78 of 78

Collection:

Collection ID:	CO004080
Collection Summary:	Blood was drawn directly into Cell-Free DNA BCT® tubes to stabilize cell-free DNA. Plasma was separated from cellular components by centrifugation. For NSCLC patients, plasma was first subjected to EGFR mutation analysis. Plasma aliquots from all participants were stored at −80°C until subsequent analysis.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR004096
Treatment Summary:	Treatment-naïve NSCLC patients had never received any systemic treatment for lung cancer. EGFR TKI-resistant NSCLC patients had evidence of disease progression according to the Response Evaluation Criteria In Solid Tumors (RECIST) version 1.1 after receiving first- or second-generation EGFR TKI treatment. All EGFR TKI-resistant NSCLC patients had acquired EGFR T790M mutation.

Sample Preparation:

Sampleprep ID:	SP004093
Sampleprep Summary:	For phospholipids extraction, 20 µL of plasma and 20 µL of 20 µM internal standard (13C-PC 16:0/16:0) was added to 150 µL of methanol, vortexed 30 sec, and mixed with 500 µL of methyl tert-butyl ether. After shaking at 2000 rpm for 30 min, 125 µL of MilliQ water was added. The mixture was incubated at room temperature for 10 min, and centrifuged at 13,800 g for 15 min at 4°C. The upper phase was collected, dried in a vacuum concentrator and reconstituted in 250 µL of 60:40 acetonitrile:water containing 0.1% formic acid. Samples were vortex for 30 sec, sonicated for 15 min, then transferred to an LC vial.

Sampleprep ID:

SP004093

Sampleprep Summary:

For phospholipids extraction, 20 µL of plasma and 20 µL of 20 µM internal standard (13C-PC 16:0/16:0) was added to 150 µL of methanol, vortexed 30 sec, and mixed with 500 µL of methyl tert-butyl ether. After shaking at 2000 rpm for 30 min, 125 µL of MilliQ water was added. The mixture was incubated at room temperature for 10 min, and centrifuged at 13,800 g for 15 min at 4°C. The upper phase was collected, dried in a vacuum concentrator and reconstituted in 250 µL of 60:40 acetonitrile:water containing 0.1% formic acid. Samples were vortex for 30 sec, sonicated for 15 min, then transferred to an LC vial.

Chromatography:

Chromatography ID:	CH004933
Instrument Name:	Waters Acquity I-Class
Column Name:	Waters ACQUITY UPLC BEH HILIC (100 x 2.1 mm, 1.7 µm)
Column Temperature:	55°C
Flow Gradient:	The gradient started at 60% A, decreased to 57% over 2 min, changed to 50% at 2.10 min, decreased to 46% at 12 min, changed to 30% at 12.10 min, decreaseding to 1% by 18 min, returneding to 60% by 20 min, and held for 3 min (total run time: 23 min)
Flow Rate:	0.3 mL/min
Solvent A:	60% Acetonitrile/40% Water; 10 mM ammonium formate ; 0.1% formic acid
Solvent B:	90% Isopropanol/10% Acetonitrile; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN006492
Analysis Type:	MS
Chromatography ID:	CH004933
Num Factors:	4
Num Metabolites:	8
Units:	umol per dL plasma