Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

David L. Tabb; Xia Wang; Steven A. Carr; Karl R. Clauser; Philipp Mertins; Matthew C. Chambers; Jerry D. Holman; Jing Wang; Bing Zhang; Lisa J. Zimmerman; Xian Chen; Harsha P. Gunawardena; Sherri R. Davies; Matthew J.C. Ellis; Shunqiang Li; R. Reid Townsend; Emily S. Boja; Karen A. Ketchum; Christopher R. Kinsinger; Mehdi Mesri; Henry Rodriguez; Tao Liu; Sangtae Kim; Jason E. McDermott; Samuel H. Payne; Vladislav A. Petyuk; Karin D. Rodland; Richard D. Smith; Feng Yang; Daniel W. Chan; Bai Zhang; Hui Zhang; Zhen Zhang; Jian Ying Zhou; Daniel C. Liebler

doi:10.1021/acs.jproteome.5b00859

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

David L. Tabb, Xia Wang, Steven A. Carr, Karl R. Clauser, Philipp Mertins, Matthew C. Chambers, Jerry D. Holman, Jing Wang, Bing Zhang, Lisa J. Zimmerman, Xian Chen, Harsha P. Gunawardena, Sherri R. Davies, Matthew J.C. Ellis, Shunqiang Li, R. Reid Townsend, Emily S. Boja, Karen A. Ketchum, Christopher R. Kinsinger, Mehdi MesriHenry Rodriguez, Tao Liu, Sangtae Kim, Jason E. McDermott, Samuel H. Payne, Vladislav A. Petyuk, Karin D. Rodland, Richard D. Smith, Feng Yang, Daniel W. Chan, Bai Zhang, Hui Zhang, Zhen Zhang, Jian Ying Zhou, Daniel C. Liebler

School of Medicine

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

31 Scopus citations

Abstract

The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.

Original language	English (US)
Pages (from-to)	691-706
Number of pages	16
Journal	Journal of proteome research
Volume	15
Issue number	3
DOIs	https://doi.org/10.1021/acs.jproteome.5b00859
State	Published - Mar 4 2016

Keywords

CPTAC
Differential proteomics
iTRAQ
label-free
quality control
technology assessment
xenografts

ASJC Scopus subject areas

General Chemistry
Biochemistry

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10.1021/acs.jproteome.5b00859

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Tabb, D. L., Wang, X., Carr, S. A., Clauser, K. R., Mertins, P., Chambers, M. C., Holman, J. D., Wang, J., Zhang, B., Zimmerman, L. J., Chen, X., Gunawardena, H. P., Davies, S. R., Ellis, M. J. C., Li, S., Townsend, R. R., Boja, E. S., Ketchum, K. A., Kinsinger, C. R., ... Liebler, D. C. (2016). Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts. Journal of proteome research, 15(3), 691-706. https://doi.org/10.1021/acs.jproteome.5b00859

Tabb, DL, Wang, X, Carr, SA, Clauser, KR, Mertins, P, Chambers, MC, Holman, JD, Wang, J, Zhang, B, Zimmerman, LJ, Chen, X, Gunawardena, HP, Davies, SR, Ellis, MJC, Li, S, Townsend, RR, Boja, ES, Ketchum, KA, Kinsinger, CR, Mesri, M, Rodriguez, H, Liu, T, Kim, S, McDermott, JE, Payne, SH, Petyuk, VA, Rodland, KD, Smith, RD, Yang, F, Chan, DW, Zhang, B, Zhang, H , Zhang, Z, Zhou, JY & Liebler, DC 2016, 'Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts', Journal of proteome research, vol. 15, no. 3, pp. 691-706. https://doi.org/10.1021/acs.jproteome.5b00859

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title = "Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts",

abstract = "The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.",

keywords = "CPTAC, Differential proteomics, iTRAQ, label-free, quality control, technology assessment, xenografts",

author = "Tabb, {David L.} and Xia Wang and Carr, {Steven A.} and Clauser, {Karl R.} and Philipp Mertins and Chambers, {Matthew C.} and Holman, {Jerry D.} and Jing Wang and Bing Zhang and Zimmerman, {Lisa J.} and Xian Chen and Gunawardena, {Harsha P.} and Davies, {Sherri R.} and Ellis, {Matthew J.C.} and Shunqiang Li and Townsend, {R. Reid} and Boja, {Emily S.} and Ketchum, {Karen A.} and Kinsinger, {Christopher R.} and Mehdi Mesri and Henry Rodriguez and Tao Liu and Sangtae Kim and McDermott, {Jason E.} and Payne, {Samuel H.} and Petyuk, {Vladislav A.} and Rodland, {Karin D.} and Smith, {Richard D.} and Feng Yang and Chan, {Daniel W.} and Bai Zhang and Hui Zhang and Zhen Zhang and Zhou, {Jian Ying} and Liebler, {Daniel C.}",

note = "Publisher Copyright: {\textcopyright} 2015 American Chemical Society.",

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doi = "10.1021/acs.jproteome.5b00859",

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T1 - Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

AU - Tabb, David L.

AU - Wang, Xia

AU - Carr, Steven A.

AU - Clauser, Karl R.

AU - Mertins, Philipp

AU - Chambers, Matthew C.

AU - Holman, Jerry D.

AU - Wang, Jing

AU - Zhang, Bing

AU - Zimmerman, Lisa J.

AU - Chen, Xian

AU - Gunawardena, Harsha P.

AU - Davies, Sherri R.

AU - Ellis, Matthew J.C.

AU - Li, Shunqiang

AU - Townsend, R. Reid

AU - Boja, Emily S.

AU - Ketchum, Karen A.

AU - Kinsinger, Christopher R.

AU - Mesri, Mehdi

AU - Rodriguez, Henry

AU - Liu, Tao

AU - Kim, Sangtae

AU - McDermott, Jason E.

AU - Payne, Samuel H.

AU - Petyuk, Vladislav A.

AU - Rodland, Karin D.

AU - Smith, Richard D.

AU - Yang, Feng

AU - Chan, Daniel W.

AU - Zhang, Bai

AU - Zhang, Hui

AU - Zhang, Zhen

AU - Zhou, Jian Ying

AU - Liebler, Daniel C.

PY - 2016/3/4

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N2 - The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.

AB - The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.

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KW - quality control

KW - technology assessment

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Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

Abstract

Keywords

ASJC Scopus subject areas

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