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.
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.affiliation: Department of Mathematical Sciences, University of Cincinnati , Cincinnati, Ohio 45221, United States.
authors.forename: Xia
authors.initials: X
authors.lastname: Wang
authors.affiliation: Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.affiliation: Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States.
authors.forename: Karl R
authors.initials: KR
authors.lastname: Clauser
authors.affiliation: Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States.
authors.forename: Philipp
authors.initials: P
authors.lastname: Mertins
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Chambers
authors.forename: Jerry D
authors.initials: JD
authors.lastname: Holman
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Zimmerman
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States.
authors.forename: Xian
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States.
authors.forename: Harsha P
authors.initials: HP
authors.lastname: Gunawardena
authors.affiliation: Department of Medicine, Washington University , St. Louis, Missouri 63110, United States.
authors.forename: Sherri R
authors.initials: SR
authors.lastname: Davies
authors.affiliation: Department of Medicine, Washington University , St. Louis, Missouri 63110, United States.
authors.forename: Matthew J C
authors.initials: MJ
authors.lastname: Ellis
authors.affiliation: Department of Medicine, Washington University , St. Louis, Missouri 63110, United States.
authors.forename: Shunqiang
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Medicine, Washington University , St. Louis, Missouri 63110, United States.
authors.forename: R Reid
authors.initials: RR
authors.lastname: Townsend
authors.affiliation: Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States.
authors.forename: Emily S
authors.initials: ES
authors.lastname: Boja
authors.affiliation: Enterprise Science and Computing, Inc. , Rockville, Maryland 20850, United States.
authors.forename: Karen A
authors.initials: KA
authors.lastname: Ketchum
authors.affiliation: Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Kinsinger
authors.affiliation: Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mesri
authors.affiliation: Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States.
authors.forename: Henry
authors.initials: H
authors.lastname: Rodriguez
authors.affiliation: Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Sangtae
authors.initials: S
authors.lastname: Kim
authors.affiliation: Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Jason E
authors.initials: JE
authors.lastname: McDermott
authors.affiliation: Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Payne
authors.affiliation: Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Vladislav A
authors.initials: VA
authors.lastname: Petyuk
authors.affiliation: Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Karin D
authors.initials: KD
authors.lastname: Rodland
authors.affiliation: Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States.
authors.forename: Feng
authors.initials: F
authors.lastname: Yang
authors.affiliation: JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States.
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Chan
authors.affiliation: JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States.
authors.forename: Bai
authors.initials: B
authors.lastname: Zhang
authors.affiliation: JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States.
authors.forename: Jian-Ying
authors.initials: JY
authors.lastname: Zhou
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Liebler
mesh_terms: D001943:Breast Neoplasms / Q000737:chemistry / Q000378:metabolism; D002853:Chromatography, Liquid; D003627:Data Interpretation, Statistical; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D064593:Heterografts / Q000737:chemistry*; D006801:Humans; D053858:Metabolic Networks and Pathways; D015588:Observer Variation; D020543:Proteome; D040901:Proteomics / Q000295:instrumentation / Q000379:methods* / Q000592:standards*; D011786:Quality Control; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry / Q000592:standards
chemical_list: D020543:Proteome
keywords: CPTAC; Differential proteomics; iTRAQ; label-free; quality control; technology assessment; xenografts