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Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts

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Item Type:Article
Title:Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts
Creators Name:Tabb, D.L. and Wang, X. and Carr, S.A. and Clauser, K.R. and Mertins, P. and Chambers, M.C. and Holman, J.D. and Wang, J. and Zhang, B. and Zimmerman, L.J. and Chen, X. and Gunawardena, H.P. and Davies, S.R. and Ellis, M.J.C. and Li, S. and Townsend, R.R. and Boja, E.S. and Ketchum, K.A. and Kinsinger, C.R. and Mesri, M. and Rodriguez, H. and Liu, T. and Kim, S. and McDermott, J.E. and Payne, S.H. and Petyuk, V.A. and Rodland, K.D. and Smith, R.D. and Yang, F. and Chan, D.W. and Zhang, B. and Zhang, H. and Zhang, Z. and Zhou, J.Y. and Liebler, D.C.
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:Differential Proteomics, Label-Free, iTRAQ, Quality Control, Xenografts, Technology Assessment, CPTAC
Source:Journal of Proteome Research
ISSN:1535-3893
Publisher:American Chemical Society (U.S.A.)
Volume:15
Number:3
Page Range:691-706
Date:4 March 2016
Official Publication:https://doi.org/10.1021/acs.jproteome.5b00859
PubMed:View item in PubMed

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