PXD010564

PXD010564 is an original dataset announced via ProteomeXchange.

Title	SISCAPA-MRM (Hsiao et al. 2017)
Description	Oral cancer is one of the most common cancers worldwide, and there are currently no biomarkers approved for aiding its management. Although many potential oral cancer biomarkers have been discovered, very few have been verified simultaneously in body fluid specimens to evaluate their clinical utility. The lack of appropriate multiplexed assays for chosen targets represents one of the bottlenecks to achieving this goal. In the present study, we develop a peptide immunoaffinity enrichment-coupled multiple reaction monitoring-mass spectrometry (SISCAPA-MRM) assay for verifying multiple reported oral cancer biomarkers in saliva. We successfully produced 363 clones of mouse anti-peptide monoclonal antibodies (mAbs) against 36 of 49 selected targets, and characterized useful mAbs against 24 targets in terms of their binding affinity for peptide antigens and immuno-capture ability. Comparative analyses revealed that an equilibrium dissociation constant (KD) cut-off value < 2.82  10-9 M could identify most clones with an immuno-capture recovery rate > 5%. Using these mAbs, we assembled a 24-plex SISCAPA -MRM assay and optimized assay conditions in a 25-g saliva matrix background. This multiplexed assay showed reasonable precision (median coefficient of variation, 7.16 to 32.09%), with lower limits of quantitation (LLOQ) of <10, 10Â?50, and >50 ng/ml for 14, 7 and 3 targets, respectively. When applied to a model saliva sample pooled from oral cancer patients, this assay could detect 19 targets at higher salivary levels than their LLOQs. Finally, we demonstrated the utility of this assay for quantification of multiple targets in individual saliva samples (20 healthy donors and 21 oral cancer patients), showing that levels of six targets were significantly altered in cancer compared with the control group. We propose that this assay could be used in future studies to compare the clinical utility of multiple oral cancer biomarker candidates in a large cohort of saliva samples.
HostingRepository	PeptideAtlas
AnnounceDate	2018-07-25
AnnouncementXML	Submission_2018-07-25_10:11:21.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yung-Chin Hsiao
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
Instrument	QTRAP 5500

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-25 10:10:02	ID requested
⏵ 1	2018-07-25 10:11:22	announced

Hsiao YC, Chi LM, Chien KY, Chiang WF, Chen SF, Chuang YN, Lin SY, Wu CC, Chang YT, Chu LJ, Chen YT, Chia SL, Chien CY, Chang KP, Chang YS, Yu JS, Development of a Multiplexed Assay for Oral Cancer Candidate Biomarkers Using Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry. Mol Cell Proteomics, 16(10):1829-1849(2017) [pubmed]

curator keyword: selected reaction monitoring, SRM, targeted

Yung-Chin Hsiao
contact affiliation	Molecular Medicine Research Center, Chang Gung University
contact email	hschin@mail.cgu.edu.tw
dataset submitter
Jau-Song Yu
contact affiliation	Department of Cell and Molecular Biology, College of Medicine, Chang Gung University
contact email	yusong@mail.cgu.edu.tw
lab head

PeptideAtlas dataset URI

PASSEL experiment URI

PASSEL transition group browser URI