Summary of Study ST003989

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	ST003989
Study Title	Plasma Amino Acids 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 gas chromatography-mass spectrometry (GC-MS), we quantified 21 amino acids 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	2025-06-02
Raw Data Available	Yes
Raw Data File Type(s)	mzML, d
Analysis Type Detail	GC-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:	SU004126
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
SA454850	C05	Plasma	Healthy	n/a	n/a
SA454851	C01	Plasma	Healthy	n/a	n/a
SA454852	C03	Plasma	Healthy	n/a	n/a
SA454853	C04	Plasma	Healthy	n/a	n/a
SA454854	C02	Plasma	Healthy	n/a	n/a
SA454855	C06	Plasma	Healthy	n/a	n/a
SA454856	C07	Plasma	Healthy	n/a	n/a
SA454857	C08	Plasma	Healthy	n/a	n/a
SA454858	C09	Plasma	Healthy	n/a	n/a
SA454859	C10	Plasma	Healthy	n/a	n/a
SA454860	B22	Plasma	NSCLC	No	Naïve
SA454861	B11	Plasma	NSCLC	No	Naïve
SA454862	B12	Plasma	NSCLC	No	Naïve
SA454863	B14	Plasma	NSCLC	No	Naïve
SA454864	B15	Plasma	NSCLC	No	Naïve
SA454865	B16	Plasma	NSCLC	No	Naïve
SA454866	B17	Plasma	NSCLC	No	Naïve
SA454867	B18	Plasma	NSCLC	No	Naïve
SA454868	B19	Plasma	NSCLC	No	Naïve
SA454869	B21	Plasma	NSCLC	No	Naïve
SA454870	B28	Plasma	NSCLC	No	Naïve
SA454871	B23	Plasma	NSCLC	No	Naïve
SA454872	B24	Plasma	NSCLC	No	Naïve
SA454873	B25	Plasma	NSCLC	No	Naïve
SA454874	B26	Plasma	NSCLC	No	Naïve
SA454875	B27	Plasma	NSCLC	No	Naïve
SA454876	B09	Plasma	NSCLC	No	Naïve
SA454877	B30	Plasma	NSCLC	No	Naïve
SA454878	B33	Plasma	NSCLC	No	Naïve
SA454879	B34	Plasma	NSCLC	No	Naïve
SA454880	B42	Plasma	NSCLC	No	Naïve
SA454881	B10	Plasma	NSCLC	No	Naïve
SA454882	B13	Plasma	NSCLC	No	Naïve
SA454883	B08	Plasma	NSCLC	No	Naïve
SA454884	B06	Plasma	NSCLC	No	Naïve
SA454885	B05	Plasma	NSCLC	No	Naïve
SA454886	B02	Plasma	NSCLC	No	Naïve
SA454887	B07	Plasma	NSCLC	No	Naïve
SA454888	B01	Plasma	NSCLC	No	Naïve
SA454889	A25	Plasma	NSCLC	Yes	Naïve
SA454890	A29	Plasma	NSCLC	Yes	Naïve
SA454891	A28	Plasma	NSCLC	Yes	Naïve
SA454892	A27	Plasma	NSCLC	Yes	Naïve
SA454893	A26	Plasma	NSCLC	Yes	Naïve
SA454894	A22	Plasma	NSCLC	Yes	Naïve
SA454895	A24	Plasma	NSCLC	Yes	Naïve
SA454896	A23	Plasma	NSCLC	Yes	Naïve
SA454897	A32	Plasma	NSCLC	Yes	Naïve
SA454898	A20	Plasma	NSCLC	Yes	Naïve
SA454899	A14	Plasma	NSCLC	Yes	Naïve
SA454900	A13	Plasma	NSCLC	Yes	Naïve
SA454901	A31	Plasma	NSCLC	Yes	Naïve
SA454902	A30	Plasma	NSCLC	Yes	Naïve
SA454903	A33	Plasma	NSCLC	Yes	Naïve
SA454904	A41	Plasma	NSCLC	Yes	Naïve
SA454905	A02	Plasma	NSCLC	Yes	Naïve
SA454906	A34	Plasma	NSCLC	Yes	Naïve
SA454907	A45	Plasma	NSCLC	Yes	Naïve
SA454908	A43	Plasma	NSCLC	Yes	Naïve
SA454909	A42	Plasma	NSCLC	Yes	Naïve
SA454910	A46	Plasma	NSCLC	Yes	Naïve
SA454911	A40	Plasma	NSCLC	Yes	Naïve
SA454912	A35	Plasma	NSCLC	Yes	Naïve
SA454913	A39	Plasma	NSCLC	Yes	Naïve
SA454914	A01	Plasma	NSCLC	Yes	Naïve
SA454915	A36	Plasma	NSCLC	Yes	Naïve
SA454916	A37	Plasma	NSCLC	Yes	Naïve
SA454917	A38	Plasma	NSCLC	Yes	Naïve
SA454918	D01	Plasma	NSCLC	Yes	TKI resistant
SA454919	D02	Plasma	NSCLC	Yes	TKI resistant
SA454920	D04	Plasma	NSCLC	Yes	TKI resistant
SA454921	D05	Plasma	NSCLC	Yes	TKI resistant
SA454922	D06	Plasma	NSCLC	Yes	TKI resistant
SA454923	D08	Plasma	NSCLC	Yes	TKI resistant
SA454924	D09	Plasma	NSCLC	Yes	TKI resistant
SA454925	D10	Plasma	NSCLC	Yes	TKI resistant
SA454926	D11	Plasma	NSCLC	Yes	TKI resistant
SA454927	D03	Plasma	NSCLC	Yes	TKI resistant

Showing results 1 to 78 of 78

Showing results 1 to 78 of 78

Collection:

Collection ID:	CO004119
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:	TR004135
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:	SP004132
Sampleprep Summary:	For free amino acids, plasma samples (50 µL) were vortexed with 4 mL of 25% acetonitrile in 0.1 M HCl for 2 min and sonicated at room temperature for 20 min., centrifuged at 9000 x g for 10 min. An aliquot (50 µL) of the supernatant was transferred to a 2 mL GC glass vial, which was added with 50 µL of norleucine (200 nmol/mL) as an internal standard. Then, the mixture was dried at 60°C about 1-2 hr, added with 50 µL dichloromethane, and dried again for 30 min. The dried samples were added with 50 µL of derivatizing agent, N-tert-Butyldimethylsilyl-N-methyltrifluoroacetamide with 1% tert-Butyldimethylchlorosilane (MTBSTFA + 1% TBDMSCl) and 50 µL of acetonitrile. The samples were sealed with an aluminum cap with PTFE/Red Rubber Septa and incubated at 100°C for 4 hr in a hot-air oven. After the sample was left at room temperature, 2 µL of the sample was analyzed by GC-MS/MS.

Sampleprep ID:

SP004132

Sampleprep Summary:

For free amino acids, plasma samples (50 µL) were vortexed with 4 mL of 25% acetonitrile in 0.1 M HCl for 2 min and sonicated at room temperature for 20 min., centrifuged at 9000 x g for 10 min. An aliquot (50 µL) of the supernatant was transferred to a 2 mL GC glass vial, which was added with 50 µL of norleucine (200 nmol/mL) as an internal standard. Then, the mixture was dried at 60°C about 1-2 hr, added with 50 µL dichloromethane, and dried again for 30 min. The dried samples were added with 50 µL of derivatizing agent, N-tert-Butyldimethylsilyl-N-methyltrifluoroacetamide with 1% tert-Butyldimethylchlorosilane (MTBSTFA + 1% TBDMSCl) and 50 µL of acetonitrile. The samples were sealed with an aluminum cap with PTFE/Red Rubber Septa and incubated at 100°C for 4 hr in a hot-air oven. After the sample was left at room temperature, 2 µL of the sample was analyzed by GC-MS/MS.

Chromatography:

Chromatography ID:	CH004987
Chromatography Summary:	The chromatographic analysis was performed on a gas chromatography (Agilent; 7890B) equipped with a mass spectrometer (Agilent, 7000D) and PAL auto sampler system. A 2 µL of sample was injected to GC-MS with split mode at a 1:5 split ratio at 280°C into a DB-5MS column (30 m, 0.25 mm id). Helium was used as a carrier gas with a constant flow rate of 1.4 mL/min. The GC oven was programmed as follows: ramp from 130°C to 190°C (6°C/min) and to 230°C (30°C/min), held at 230°C for 5 min, then ramp to 325 °C, and held at 325°C for 6 min. The transfer line, ion source, and quadrupole were set as 325°C, 240°C, and 180 °C, respectively.
Instrument Name:	Agilent 6890N
Column Name:	Agilent DB5-MS (30 m x 0.25 mm, 0.25 µm)
Column Temperature:	not applicable
Flow Gradient:	not applicable
Flow Rate:	1.4 mL/min
Solvent A:	not applicable
Solvent B:	not applicable
Chromatography Type:	GC

Analysis:

Analysis ID:	AN006570
Analysis Type:	MS
Chromatography ID:	CH004987
Num Factors:	4
Num Metabolites:	21
Units:	micro molar