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 Fenyö; Tara 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 N Thomas; R. Reid Townsend; Gordon Whiteley; Chaochao Wu; Hui Zhang; Zhen Zhang; Henry Rodriguez; Amanda G. Paulovich

doi:10.1007/978-1-4939-3524-6_13

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 N Thomas, R. Reid Townsend, Gordon Whiteley, Chaochao Wu, Hui Zhang, Zhen Zhang, Henry Rodriguez, Amanda G. Paulovich

School of Medicine

Research output: Contribution to journal › Article › peer-review

19 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 language	English (US)
Pages (from-to)	223-236
Number of pages	14
Journal	Methods in Molecular Biology
Volume	1410
DOIs	https://doi.org/10.1007/978-1-4939-3524-6_13
State	Published - Feb 1 2016

Keywords

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

ASJC Scopus subject areas

Molecular Biology
Genetics

Access to Document

10.1007/978-1-4939-3524-6_13

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

Whiteaker, JR, Halusa, GN, Hoofnagle, AN, Sharma, V, MacLean, B, Yan, P, Wrobel, JA, Kennedy, J, Mani, DR, Zimmerman, LJ, Meyer, MR, Mesri, M, 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, Liu, T, Loss, M, Maccoss, MJ, Qian, WJ, Rivers, R, Rodland, KD, Ruggles, KV, Scott, MG, Smith, RD, Thomas, SN, Townsend, RR, Whiteley, G, Wu, C, Zhang, H , Zhang, Z, Rodriguez, H & Paulovich, AG 2016, 'Using the cptac assay portal to identify and implement highly characterized targeted proteomics assays', Methods in Molecular Biology, vol. 1410, pp. 223-236. https://doi.org/10.1007/978-1-4939-3524-6_13

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title = "Using the cptac assay portal to identify and implement highly characterized targeted proteomics assays",

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.",

keywords = "Harmonization, MRM, Multiple reaction monitoring, PRM, Quantitative assay database, Quantitative proteomics, SRM, Selected reaction monitoring, Standardization, Targeted mass spectrometry",

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 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 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 Thomas, {Stefani N} and Townsend, {R. Reid} and Gordon Whiteley and Chaochao Wu and Hui Zhang and Zhen Zhang and Henry Rodriguez and Paulovich, {Amanda G.}",

note = "Publisher Copyright: {\textcopyright} Springer Science+Business Media New York 2016.",

year = "2016",

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doi = "10.1007/978-1-4939-3524-6_13",

language = "English (US)",

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pages = "223--236",

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T1 - Using the cptac assay portal to identify and implement highly characterized targeted proteomics 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 - 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 - 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 N

AU - Townsend, R. Reid

AU - Whiteley, Gordon

AU - Wu, Chaochao

AU - Zhang, Hui

AU - Zhang, Zhen

AU - Rodriguez, Henry

AU - Paulovich, Amanda G.

PY - 2016/2/1

Y1 - 2016/2/1

N2 - 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.

AB - 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.

KW - Harmonization

KW - MRM

KW - Multiple reaction monitoring

KW - PRM

KW - Quantitative assay database

KW - Quantitative proteomics

KW - SRM

KW - Selected reaction monitoring

KW - Standardization

KW - Targeted mass spectrometry

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U2 - 10.1007/978-1-4939-3524-6_13

DO - 10.1007/978-1-4939-3524-6_13

M3 - Article

C2 - 26867747

AN - SCOPUS:84958538013

SN - 1064-3745

VL - 1410

SP - 223

EP - 236

JO - Methods in Molecular Biology

JF - Methods in Molecular Biology

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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