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 Chen; Sherri 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

doi:10.1038/nmeth.3002

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 journal › Letter › peer-review

148 Scopus citations

Original language	English
Pages (from-to)	703-704
Number of pages	2
Journal	Nature Methods
Volume	11
Issue number	7
DOIs	https://doi.org/10.1038/nmeth.3002
State	Published - Jul 2014

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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., Rodriguez, H., Paulovich, A. G., Abbatiello, S. E., Boja, E., Carr, S. A., Chan, D. W., Chen, X., ... Zhang, Z. (2014). CPTAC Assay Portal: A repository of targeted proteomic assays. Nature Methods, 11(7), 703-704. https://doi.org/10.1038/nmeth.3002

@article{e9921d19e1d64102a4d388f4a302ae8d,

title = "CPTAC Assay Portal: A repository of targeted proteomic assays",

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

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 {\textquoteleft}fit-for-purpose{\textquoteright} 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 {\textquoteleft}Tier 2{\textquoteright} 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.",

year = "2014",

month = jul,

doi = "10.1038/nmeth.3002",

language = "English",

volume = "11",

pages = "703--704",

journal = "Nature Methods",

issn = "1548-7091",

number = "7",

}

Whiteaker, JR, Halusa, GN, Hoofnagle, AN, Sharma, V, MacLean, B, Yan, P, Wrobel, JA, Kennedy, J, Mani, DR, Zimmerman, LJ, Meyer, MR, Mesri, M, Rodriguez, H, Paulovich, AG, Abbatiello, SE, Boja, E, Carr, SA, Chan, DW, Chen, X, Chen, J, Davies, SR, Ellis, MJC, Fenyö, D, Hiltke, T, Ketchum, KA, Kinsinger, C, Kuhn, E, Liebler, DC, Lin, D, Liu, T, Loss, M, MacCoss, MJ, Qian, WJ, Rivers, R, Rodland, KD, Ruggles, KV, Scott, MG, Smith, RD, Thomas, S, Townsend, RR, Whiteley, G, Wu, C, Zhang, H & Zhang, Z 2014, 'CPTAC Assay Portal: A repository of targeted proteomic assays', Nature Methods, vol. 11, no. 7, pp. 703-704. https://doi.org/10.1038/nmeth.3002

TY - JOUR

T1 - CPTAC Assay Portal

T2 - A repository of targeted proteomic assays

AU - Whiteaker, Jeffrey R.

AU - Halusa, Goran N.

AU - Hoofnagle, Andrew N.

AU - Sharma, Vagisha

AU - MacLean, Brendan

AU - Yan, Ping

AU - Wrobel, John A.

AU - Kennedy, Jacob

AU - Mani, D. R.

AU - Zimmerman, Lisa J.

AU - Meyer, Matthew R.

AU - Mesri, Mehdi

AU - Rodriguez, Henry

AU - Paulovich, Amanda G.

AU - Abbatiello, Susan E.

AU - Boja, Emily

AU - Carr, Steven A.

AU - Chan, Daniel W.

AU - Chen, Xian

AU - Chen, Jing

AU - Davies, Sherri R.

AU - Ellis, Matthew J.C.

AU - Fenyö, David

AU - Hiltke, Tara

AU - Ketchum, Karen A.

AU - Kinsinger, Chris

AU - Kuhn, Eric

AU - Liebler, Daniel C.

AU - Lin, De

AU - Liu, Tao

AU - Loss, Michael

AU - MacCoss, Michael J.

AU - Qian, Wei Jun

AU - Rivers, Robert

AU - Rodland, Karin D.

AU - Ruggles, Kelly V.

AU - Scott, Mitchell G.

AU - Smith, Richard D.

AU - Thomas, Stefani

AU - Townsend, R. Reid

AU - Whiteley, Gordon

AU - Wu, Chaochao

AU - Zhang, Hui

AU - Zhang, Zhen

N1 - 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.

PY - 2014/7

Y1 - 2014/7

UR - http://www.scopus.com/inward/record.url?scp=84903542932&partnerID=8YFLogxK

U2 - 10.1038/nmeth.3002

DO - 10.1038/nmeth.3002

M3 - Letter

C2 - 24972168

AN - SCOPUS:84903542932

SN - 1548-7091

VL - 11

SP - 703

EP - 704

JO - Nature Methods

JF - Nature Methods

IS - 7

ER -

CPTAC Assay Portal: A repository of targeted proteomic assays

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