Summary of Study ST004184

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	ST004184
Study Title	Plasma Sugar and Sugar Alcohols 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 18 sugar and sugar alcohols of 78 individuals, including NSCLC patients and healthy controls.
Institute	Mahidol University
Last Name	Khoomrung
First Name	Sakda
Address	2 Wanglang road, Bangkok noi, bangkok, 10700, Thailand
Email	Sakda.kho@mahidol.edu
Phone	6624195505
Submit Date	2025-09-09
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	GC-MS
Release Date	2025-10-06
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:	SU004335
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

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
SA482772	C05	Plasma	Healthy	n/a	n/a
SA482773	C01	Plasma	Healthy	n/a	n/a
SA482774	C03	Plasma	Healthy	n/a	n/a
SA482775	C04	Plasma	Healthy	n/a	n/a
SA482776	C02	Plasma	Healthy	n/a	n/a
SA482777	C06	Plasma	Healthy	n/a	n/a
SA482778	C07	Plasma	Healthy	n/a	n/a
SA482779	C08	Plasma	Healthy	n/a	n/a
SA482780	C09	Plasma	Healthy	n/a	n/a
SA482781	C10	Plasma	Healthy	n/a	n/a
SA482782	B22	Plasma	NSCLC	No	Naïve
SA482783	B11	Plasma	NSCLC	No	Naïve
SA482784	B12	Plasma	NSCLC	No	Naïve
SA482785	B14	Plasma	NSCLC	No	Naïve
SA482786	B15	Plasma	NSCLC	No	Naïve
SA482787	B16	Plasma	NSCLC	No	Naïve
SA482788	B17	Plasma	NSCLC	No	Naïve
SA482789	B18	Plasma	NSCLC	No	Naïve
SA482790	B19	Plasma	NSCLC	No	Naïve
SA482791	B21	Plasma	NSCLC	No	Naïve
SA482792	B28	Plasma	NSCLC	No	Naïve
SA482793	B23	Plasma	NSCLC	No	Naïve
SA482794	B24	Plasma	NSCLC	No	Naïve
SA482795	B25	Plasma	NSCLC	No	Naïve
SA482796	B26	Plasma	NSCLC	No	Naïve
SA482797	B27	Plasma	NSCLC	No	Naïve
SA482798	B09	Plasma	NSCLC	No	Naïve
SA482799	B30	Plasma	NSCLC	No	Naïve
SA482800	B33	Plasma	NSCLC	No	Naïve
SA482801	B34	Plasma	NSCLC	No	Naïve
SA482802	B42	Plasma	NSCLC	No	Naïve
SA482803	B10	Plasma	NSCLC	No	Naïve
SA482804	B13	Plasma	NSCLC	No	Naïve
SA482805	B08	Plasma	NSCLC	No	Naïve
SA482806	B06	Plasma	NSCLC	No	Naïve
SA482807	B05	Plasma	NSCLC	No	Naïve
SA482808	B02	Plasma	NSCLC	No	Naïve
SA482809	B07	Plasma	NSCLC	No	Naïve
SA482810	B01	Plasma	NSCLC	No	Naïve
SA482811	A25	Plasma	NSCLC	Yes	Naïve
SA482812	A29	Plasma	NSCLC	Yes	Naïve
SA482813	A28	Plasma	NSCLC	Yes	Naïve
SA482814	A27	Plasma	NSCLC	Yes	Naïve
SA482815	A26	Plasma	NSCLC	Yes	Naïve
SA482816	A22	Plasma	NSCLC	Yes	Naïve
SA482817	A24	Plasma	NSCLC	Yes	Naïve
SA482818	A23	Plasma	NSCLC	Yes	Naïve
SA482819	A32	Plasma	NSCLC	Yes	Naïve
SA482820	A20	Plasma	NSCLC	Yes	Naïve
SA482821	A14	Plasma	NSCLC	Yes	Naïve
SA482822	A13	Plasma	NSCLC	Yes	Naïve
SA482823	A31	Plasma	NSCLC	Yes	Naïve
SA482824	A30	Plasma	NSCLC	Yes	Naïve
SA482825	A33	Plasma	NSCLC	Yes	Naïve
SA482826	A41	Plasma	NSCLC	Yes	Naïve
SA482827	A02	Plasma	NSCLC	Yes	Naïve
SA482828	A34	Plasma	NSCLC	Yes	Naïve
SA482829	A45	Plasma	NSCLC	Yes	Naïve
SA482830	A43	Plasma	NSCLC	Yes	Naïve
SA482831	A42	Plasma	NSCLC	Yes	Naïve
SA482832	A46	Plasma	NSCLC	Yes	Naïve
SA482833	A40	Plasma	NSCLC	Yes	Naïve
SA482834	A35	Plasma	NSCLC	Yes	Naïve
SA482835	A39	Plasma	NSCLC	Yes	Naïve
SA482836	A01	Plasma	NSCLC	Yes	Naïve
SA482837	A36	Plasma	NSCLC	Yes	Naïve
SA482838	A37	Plasma	NSCLC	Yes	Naïve
SA482839	A38	Plasma	NSCLC	Yes	Naïve
SA482840	D01	Plasma	NSCLC	Yes	TKI resistant
SA482841	D02	Plasma	NSCLC	Yes	TKI resistant
SA482842	D04	Plasma	NSCLC	Yes	TKI resistant
SA482843	D05	Plasma	NSCLC	Yes	TKI resistant
SA482844	D06	Plasma	NSCLC	Yes	TKI resistant
SA482845	D08	Plasma	NSCLC	Yes	TKI resistant
SA482846	D09	Plasma	NSCLC	Yes	TKI resistant
SA482847	D10	Plasma	NSCLC	Yes	TKI resistant
SA482848	D11	Plasma	NSCLC	Yes	TKI resistant
SA482849	D03	Plasma	NSCLC	Yes	TKI resistant

Showing results 1 to 78 of 78

Showing results 1 to 78 of 78

Collection:

Collection ID:	CO004328
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:	TR004344
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:	SP004341
Sampleprep Summary:	For sugar alcohol, 50 µL of plasma was extracted with 400 µL of methanol in a 1.5 ml Eppendorf tube, vortexed at 2,200 rpm for 10 min (three times), then centrifuged at 10,000 x g for 10 min (4°C) using a centrifuge (5810R, Eppendorf, USA). A 100 µL of supernatant was transferred into a 2-ml GC glass vial, and 20 µL of 1µmol/mL of internal standard (myristic acid-D27) in hexane was added. The mixture was dried at 60°C for 2 hours using a vacuum concentrator (Concentrator plus, Eppendorf, USA), then added with 50 µl dichloromethane and dried again for 30 min. Subsequently, a 50 µL of 40 mg/mL of O-methyl hydroxylamine hydrochloride in pyridine was added to the dried sample for a methoxylation reaction. The reaction was performed under 30 °C for 90 min. For trimethylsilylation reaction, a 50 µL of N-trimethyl-N-methyl trifluoroacetamide containing 1% of trimethylchlorosilane (MSTFA + 1% TMCS) was added into the mixtures and incubated at 37 °C for 30 min. The derivatized samples were cooled at room temperature and immediately for GC/MS analysis.

Sampleprep ID:

SP004341

Sampleprep Summary:

For sugar alcohol, 50 µL of plasma was extracted with 400 µL of methanol in a 1.5 ml Eppendorf tube, vortexed at 2,200 rpm for 10 min (three times), then centrifuged at 10,000 x g for 10 min (4°C) using a centrifuge (5810R, Eppendorf, USA). A 100 µL of supernatant was transferred into a 2-ml GC glass vial, and 20 µL of 1µmol/mL of internal standard (myristic acid-D27) in hexane was added. The mixture was dried at 60°C for 2 hours using a vacuum concentrator (Concentrator plus, Eppendorf, USA), then added with 50 µl dichloromethane and dried again for 30 min. Subsequently, a 50 µL of 40 mg/mL of O-methyl hydroxylamine hydrochloride in pyridine was added to the dried sample for a methoxylation reaction. The reaction was performed under 30 °C for 90 min. For trimethylsilylation reaction, a 50 µL of N-trimethyl-N-methyl trifluoroacetamide containing 1% of trimethylchlorosilane (MSTFA + 1% TMCS) was added into the mixtures and incubated at 37 °C for 30 min. The derivatized samples were cooled at room temperature and immediately for GC/MS analysis.

Chromatography:

Chromatography ID:	CH005273
Chromatography Summary:	The sample was analyzed by a gas chromatography-quadrupole time of flight mass spectrometer (GC/Q-TOF, GC 7890B/MSD 7250, Agilent Technologies, USA) coupled to the PAL autosampler system (CTC Analytics AG, Switzerland). An aliquot of 2 µl was injected into GC/Q-TOFMS using split mode with an injector temperature of 250°C, a split ratio of 10 to 1, and a DB-5MS UI column (30 m, 0.25 mm i.d., Agilent Technologies, USA). Helium was used as a carrier gas with a constant flow rate of 1.0 ml/min. The GC oven was programmed as follows: The initial oven temperature was controlled at 60°C, help for 1 min. Then, the temperature was ramped from 60 °C to 325 °C at the rate of 10 °C/min and held for 10 min. The total run time was 37.5 min. The transfer line, ion source, and quadrupole were set as 325 °C, 240 °C, and 180 °C, respectively.
Instrument Name:	Agilent GC7890B
Column Name:	DB-5MS UI column (30 m, 0.25 mm i.d.)
Column Temperature:	not applicable
Flow Gradient:	not applicable
Flow Rate:	1.0 ml/min
Solvent A:	not applicable
Solvent B:	not applicable
Chromatography Type:	GC

Analysis:

Analysis ID:	AN006947
Analysis Type:	MS
Chromatography ID:	CH005273
Num Factors:	4
Num Metabolites:	8
Units:	micro molar