CPTAC Assay Portal: A repository of targeted proteomic 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, Henry Rodriguez, Amanda G. Paulovich, Susan E. Abbatiello, Emily Boja, Steven A. Carr, Daniel W. Chan, Xian Chen, Jing ChenSherri R. Davies, Matthew J.C. Ellis, David Fenyö, Tara Hiltke, Karen A. Ketchum, Chris Kinsinger, Eric Kuhn, Daniel C. Liebler, De Lin, 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

Research output: Contribution to journalLetterpeer-review

84 Scopus citations
Original languageEnglish (US)
Pages (from-to)703-704
Number of pages2
JournalNature Methods
Issue number7
StatePublished - Jul 2014
Externally publishedYes

Bibliographical note

Funding Information:
This work was funded by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the US National Cancer Institute under grant nos. U24CA160034 (S.A.C., A.G.P.), U24CA160036 (D.W.C.), U24CA160019 (R.D.S., K.D.R.), U24CA159988 (D.C.L.) and U24CA160035 (M.J.C.E.), as well as US National Institutes of Health grant nos. R01GM103551 (M.J.M.) and U01CA164186 (M.J.M.).

Funding Information:
Data quality is a key emphasis and distinguishing feature of the portal. A framework for MRM assay ‘fit-for-purpose’ validation has been established by CPTAC, with input from the outside community solicited via a workshop jointly sponsored by the NCI and the National Heart, Lung, and Blood Institute4. Assays presented on the portal predominantly represent ‘Tier 2’ assays, as described in the workshop report. To ensure sufficient assay characterization and data quality, a guidance document describing the minimal characterization data required for assay inclusion in the CPTAC Assay Portal is available for download (https://assays.cancer.gov/guidance-document/). This guidance document outlines a list of characterizations that will help potential downstream users evaluate the utility of adopting and deploying the assays in their own work. Five experiments are outlined (Fig. 1b); experiments 1 and 2 are required for upload. Assays are entered through a web-based entry form and the uploading of data to Panorama. Characterization experiments are analyzed by scripts available through Panorama. Uploaded assays are subjected to manual review by site administrators to ensure data quality and the fulfillment of minimum requirements for assay characterization.

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