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Title: Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer

Here, mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are becoming the method of choice for preclinical verification of candidate protein biomarkers. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large set of targeted MS-based assays, and a depository to share assays publicly, providing that assays meet the guidelines proposed by CPTAC. Herein, we report 98 SRM assays covering 70 candidate protein biomarkers previously reported as associated with ovarian cancer that have been thoroughly characterized according to the CPTAC Assay Characterization Guidance Document. The experiments, methods and results for characterizing these SRM assays for their MS response, repeatability, selectivity, stability, and reproducible detection of endogenous analytes are described in detail.
Authors:
 [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [1] ;  [1] ; ORCiD logo [1] ; ORCiD logo [1] ;  [1] ;  [1]
  1. Biological Sciences Div., Richland, WA (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Report Number(s):
PNNL-SA-122408
Journal ID: ISSN 2052-4463; 48666; 453040220
Grant/Contract Number:
AC05-76RL01830
Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; Environmental Molecular Sciences Laboratory
OSTI Identifier:
1375373

Song, Ehwang, Gao, Yuqian, Wu, Chaochao, Shi, Tujin, Nie, Song, Fillmore, Thomas L., Schepmoes, Athena A., Gritsenko, Marina A., Qian, Wei -Jun, Smith, Richard D., Rodland, Karin D., and Liu, Tao. Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. United States: N. p., Web. doi:10.1038/sdata.2017.91.
Song, Ehwang, Gao, Yuqian, Wu, Chaochao, Shi, Tujin, Nie, Song, Fillmore, Thomas L., Schepmoes, Athena A., Gritsenko, Marina A., Qian, Wei -Jun, Smith, Richard D., Rodland, Karin D., & Liu, Tao. Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. United States. doi:10.1038/sdata.2017.91.
Song, Ehwang, Gao, Yuqian, Wu, Chaochao, Shi, Tujin, Nie, Song, Fillmore, Thomas L., Schepmoes, Athena A., Gritsenko, Marina A., Qian, Wei -Jun, Smith, Richard D., Rodland, Karin D., and Liu, Tao. 2017. "Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer". United States. doi:10.1038/sdata.2017.91. https://www.osti.gov/servlets/purl/1375373.
@article{osti_1375373,
title = {Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer},
author = {Song, Ehwang and Gao, Yuqian and Wu, Chaochao and Shi, Tujin and Nie, Song and Fillmore, Thomas L. and Schepmoes, Athena A. and Gritsenko, Marina A. and Qian, Wei -Jun and Smith, Richard D. and Rodland, Karin D. and Liu, Tao},
abstractNote = {Here, mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are becoming the method of choice for preclinical verification of candidate protein biomarkers. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large set of targeted MS-based assays, and a depository to share assays publicly, providing that assays meet the guidelines proposed by CPTAC. Herein, we report 98 SRM assays covering 70 candidate protein biomarkers previously reported as associated with ovarian cancer that have been thoroughly characterized according to the CPTAC Assay Characterization Guidance Document. The experiments, methods and results for characterizing these SRM assays for their MS response, repeatability, selectivity, stability, and reproducible detection of endogenous analytes are described in detail.},
doi = {10.1038/sdata.2017.91},
journal = {Scientific Data},
number = ,
volume = 4,
place = {United States},
year = {2017},
month = {7}
}