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Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts
[Image: see text] 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 l...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2015
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779376/ https://www.ncbi.nlm.nih.gov/pubmed/26653538 http://dx.doi.org/10.1021/acs.jproteome.5b00859 |
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author | Tabb, David L. Wang, Xia Carr, Steven A. Clauser, Karl R. Mertins, Philipp Chambers, Matthew C. Holman, Jerry D. Wang, Jing Zhang, Bing Zimmerman, Lisa J. Chen, Xian Gunawardena, Harsha P. Davies, Sherri R. Ellis, Matthew J. C. Li, Shunqiang Townsend, R. Reid Boja, Emily S. Ketchum, Karen A. Kinsinger, Christopher R. Mesri, Mehdi Rodriguez, Henry Liu, Tao Kim, Sangtae McDermott, Jason E. Payne, Samuel H. Petyuk, Vladislav A. Rodland, Karin D. Smith, Richard D. Yang, Feng Chan, Daniel W. Zhang, Bai Zhang, Hui Zhang, Zhen Zhou, Jian-Ying Liebler, Daniel C. |
author_facet | Tabb, David L. Wang, Xia Carr, Steven A. Clauser, Karl R. Mertins, Philipp Chambers, Matthew C. Holman, Jerry D. Wang, Jing Zhang, Bing Zimmerman, Lisa J. Chen, Xian Gunawardena, Harsha P. Davies, Sherri R. Ellis, Matthew J. C. Li, Shunqiang Townsend, R. Reid Boja, Emily S. Ketchum, Karen A. Kinsinger, Christopher R. Mesri, Mehdi Rodriguez, Henry Liu, Tao Kim, Sangtae McDermott, Jason E. Payne, Samuel H. Petyuk, Vladislav A. Rodland, Karin D. Smith, Richard D. Yang, Feng Chan, Daniel W. Zhang, Bai Zhang, Hui Zhang, Zhen Zhou, Jian-Ying Liebler, Daniel C. |
author_sort | Tabb, David L. |
collection | PubMed |
description | [Image: see text] 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. |
format | Online Article Text |
id | pubmed-4779376 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-47793762016-03-09 Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts Tabb, David L. Wang, Xia Carr, Steven A. Clauser, Karl R. Mertins, Philipp Chambers, Matthew C. Holman, Jerry D. Wang, Jing Zhang, Bing Zimmerman, Lisa J. Chen, Xian Gunawardena, Harsha P. Davies, Sherri R. Ellis, Matthew J. C. Li, Shunqiang Townsend, R. Reid Boja, Emily S. Ketchum, Karen A. Kinsinger, Christopher R. Mesri, Mehdi Rodriguez, Henry Liu, Tao Kim, Sangtae McDermott, Jason E. Payne, Samuel H. Petyuk, Vladislav A. Rodland, Karin D. Smith, Richard D. Yang, Feng Chan, Daniel W. Zhang, Bai Zhang, Hui Zhang, Zhen Zhou, Jian-Ying Liebler, Daniel C. J Proteome Res [Image: see text] 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. American Chemical Society 2015-12-14 2016-03-04 /pmc/articles/PMC4779376/ /pubmed/26653538 http://dx.doi.org/10.1021/acs.jproteome.5b00859 Text en Copyright © 2015 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes. |
spellingShingle | Tabb, David L. Wang, Xia Carr, Steven A. Clauser, Karl R. Mertins, Philipp Chambers, Matthew C. Holman, Jerry D. Wang, Jing Zhang, Bing Zimmerman, Lisa J. Chen, Xian Gunawardena, Harsha P. Davies, Sherri R. Ellis, Matthew J. C. Li, Shunqiang Townsend, R. Reid Boja, Emily S. Ketchum, Karen A. Kinsinger, Christopher R. Mesri, Mehdi Rodriguez, Henry Liu, Tao Kim, Sangtae McDermott, Jason E. Payne, Samuel H. Petyuk, Vladislav A. Rodland, Karin D. Smith, Richard D. Yang, Feng Chan, Daniel W. Zhang, Bai Zhang, Hui Zhang, Zhen Zhou, Jian-Ying Liebler, Daniel C. Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts |
title | Reproducibility
of Differential Proteomic Technologies
in CPTAC Fractionated Xenografts |
title_full | Reproducibility
of Differential Proteomic Technologies
in CPTAC Fractionated Xenografts |
title_fullStr | Reproducibility
of Differential Proteomic Technologies
in CPTAC Fractionated Xenografts |
title_full_unstemmed | Reproducibility
of Differential Proteomic Technologies
in CPTAC Fractionated Xenografts |
title_short | Reproducibility
of Differential Proteomic Technologies
in CPTAC Fractionated Xenografts |
title_sort | reproducibility
of differential proteomic technologies
in cptac fractionated xenografts |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779376/ https://www.ncbi.nlm.nih.gov/pubmed/26653538 http://dx.doi.org/10.1021/acs.jproteome.5b00859 |
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