Using the cptac assay portal to identify and implement highly characterized targeted proteomics assays

Jeffrey R. Whiteaker, Goran N. Halusa, Andrew N. Hoofnagle, Vagisha Sharma, Brendan MacLean, Ping Yan, John A. Wrobel, Jacob Kennedy, D. R. Mani, Lisa J. Zimmerman, Matthew R. Meyer, Mehdi Mesri, Emily Boja, Steven A. Carr, Daniel W. Chan, Xian Chen, Jing Chen, Sherri R. Davies, Matthew J.C. Ellis, David FenyöTara Hiltke, Karen A. Ketchum, Chris Kinsinger, Eric Kuhn, Daniel C. Liebler, Tao Liu, Michael Loss, Michael J. Maccoss, Wei Jun Qian, Robert Rivers, Karin D. Rodland, Kelly V. Ruggles, Mitchell G. Scott, Richard D. Smith, Stefani Thomas, R. Reid Townsend, Gordon Whiteley, Chaochao Wu, Hui Zhang, Zhen Zhang, Henry Rodriguez, Amanda G. Paulovich

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as an open-source repository of well characterized targeted proteomic assays. The portal is designed to curate and disseminate highly characterized, targeted mass spectrometry (MS)-based assays by providing detailed assay performance characterization data, standard operating procedures, and access to reagents. Assay content is accessed via the portal through queries to find assays targeting proteins associated with specific cellular pathways, protein complexes, or specific chromosomal regions. The position of the peptide analytes for which there are available assays are mapped relative to other features of interest in the protein, such as sequence domains, isoforms, single nucleotide polymorphisms, and posttranslational modifications. The overarching goals are to enable robust quantification of all human proteins and to standardize the quantification of targeted MS-based assays to ultimately enable harmonization of results over time and across laboratories.

Original languageEnglish (US)
Pages (from-to)223-236
Number of pages14
JournalMethods in Molecular Biology
Volume1410
DOIs
StatePublished - Feb 1 2016
Externally publishedYes

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Keywords

  • Harmonization
  • MRM
  • Multiple reaction monitoring
  • PRM
  • Quantitative assay database
  • Quantitative proteomics
  • SRM
  • Selected reaction monitoring
  • Standardization
  • Targeted mass spectrometry

Cite this

Whiteaker, J. R., Halusa, G. N., Hoofnagle, A. N., Sharma, V., MacLean, B., Yan, P., Wrobel, J. A., Kennedy, J., Mani, D. R., Zimmerman, L. J., Meyer, M. R., Mesri, M., Boja, E., Carr, S. A., Chan, D. W., Chen, X., Chen, J., Davies, S. R., Ellis, M. J. C., ... Paulovich, A. G. (2016). Using the cptac assay portal to identify and implement highly characterized targeted proteomics assays. Methods in Molecular Biology, 1410, 223-236. https://doi.org/10.1007/978-1-4939-3524-6_13