PXD004384-2

PXD004384 is an original dataset announced via ProteomeXchange.

Title	MRM analysis of serological markers for lung cancer
Description	Non-small cell lung cancer (NSCLC) constitutes approximately 80% of all diagnosed lung cancers and diagnostic markers detectable in the plasma/serum of NSCLC patients are greatly needed. Omic-based platforms have been promoted for the discovery of disease biomarkers. In this study, we established a pipeline for the discovery of markers using 10 transcriptome data sets obtained from the Gene Expression Omnibus (GEO) and the profiling of six lung cancer cell secretomes. Seventeen out of 281 proteins that overlapped between ±15% differentially expressed genes and identified cell secretome proteins were detected in the pooled plasma of lung cancer patients. In the verification process, 58 signature peptides for 17 candidates were first confirmed by Qtrap5500. To quantify the candidates in the serum of NSCLC patients, multiple reaction monitoring mass spectrometry (MRM-MS) with stable isotope-labeled standard (SIS) peptides was performed for eight candidate biomarkers. Finally, two potential biomarkers (BCHE and GPX3; AUC = 0.918 and 0.728, respectively) and one two-marker panel (BCHE/GPX3; AUC = 0.943) were able to effectively differentiate NSCLC from healthy controls. Collectively, these results demonstrate that our pipeline for marker discovery and our MRM-MS platform for verifying potential biomarkers are feasible for use with human diseases.
HostingRepository	PeptideAtlas
AnnounceDate	2016-06-20
AnnouncementXML	Submission_2016-06-20_15:51:58.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Heesung Ahn
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	6x(13)C,4x(15)N labeled L-arginine; 6x(13)C,2x(15)N labeled L-lysine; S-carboxamidomethyl-L-cysteine
Instrument	QTRAP 5500

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-20 15:00:28	ID requested
1	2016-06-20 15:36:40	announced
⏵ 2	2016-06-20 15:51:59	announced	update

Jihye, et al. (submitted)

curator keyword: selected reaction monitoring, SRM, targeted

Heesung Ahn
contact affiliation	Korea Institute of Science and Technology
contact email	zaulim3@gmail.com
dataset submitter
Cheolju Lee
contact affiliation	Korea Institute of Science and Technology
contact email	clee270@kist.re.kr
lab head

PeptideAtlas dataset URI

PASSEL experiment URI

PASSEL transition group browser URI