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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. Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts. J Proteome Res 2015; 15:691-706. [PMID: 26653538 PMCID: PMC4779376 DOI: 10.1021/acs.jproteome.5b00859] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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.
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Affiliation(s)
| | - Xia Wang
- Department of Mathematical Sciences, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Karl R Clauser
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Philipp Mertins
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | | | | | | | | | | | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Harsha P Gunawardena
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Sherri R Davies
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Matthew J C Ellis
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Shunqiang Li
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - R Reid Townsend
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Karen A Ketchum
- Enterprise Science and Computing, Inc. , Rockville, Maryland 20850, United States
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Tao Liu
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Sangtae Kim
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Jason E McDermott
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Samuel H Payne
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Vladislav A Petyuk
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Karin D Rodland
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Richard D Smith
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Feng Yang
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Daniel W Chan
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Bai Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Hui Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Zhen Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Jian-Ying Zhou
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
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Barsan C, Zouine M, Maza E, Bian W, Egea I, Rossignol M, Bouyssie D, Pichereaux C, Purgatto E, Bouzayen M, Latché A, Pech JC. Proteomic analysis of chloroplast-to-chromoplast transition in tomato reveals metabolic shifts coupled with disrupted thylakoid biogenesis machinery and elevated energy-production components. PLANT PHYSIOLOGY 2012; 160:708-25. [PMID: 22908117 PMCID: PMC3461550 DOI: 10.1104/pp.112.203679] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 08/16/2012] [Indexed: 05/18/2023]
Abstract
A comparative proteomic approach was performed to identify differentially expressed proteins in plastids at three stages of tomato (Solanum lycopersicum) fruit ripening (mature-green, breaker, red). Stringent curation and processing of the data from three independent replicates identified 1,932 proteins among which 1,529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immunoblot analysis of six proteins representative of distinct metabolic or regulatory pathways. Among the main features of the chloroplast-to-chromoplast transition revealed by the study, chromoplastogenesis appears to be associated with major metabolic shifts: (1) strong decrease in abundance of proteins of light reactions (photosynthesis, Calvin cycle, photorespiration) and carbohydrate metabolism (starch synthesis/degradation), mostly between breaker and red stages and (2) increase in terpenoid biosynthesis (including carotenoids) and stress-response proteins (ascorbate-glutathione cycle, abiotic stress, redox, heat shock). These metabolic shifts are preceded by the accumulation of plastid-encoded acetyl Coenzyme A carboxylase D proteins accounting for the generation of a storage matrix that will accumulate carotenoids. Of particular note is the high abundance of proteins involved in providing energy and in metabolites import. Structural differentiation of the chromoplast is characterized by a sharp and continuous decrease of thylakoid proteins whereas envelope and stroma proteins remain remarkably stable. This is coincident with the disruption of the machinery for thylakoids and photosystem biogenesis (vesicular trafficking, provision of material for thylakoid biosynthesis, photosystems assembly) and the loss of the plastid division machinery. Altogether, the data provide new insights on the chromoplast differentiation process while enriching our knowledge of the plant plastid proteome.
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Affiliation(s)
| | | | | | | | - Isabel Egea
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Michel Rossignol
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - David Bouyssie
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Carole Pichereaux
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Eduardo Purgatto
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Mondher Bouzayen
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Alain Latché
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
| | - Jean-Claude Pech
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Génomique et Biotechnologie des Fruits, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Institut National de la Recherche Agronomique, Génomique et Biotechnologie des Fruits, Chemin de Borde Rouge, Castanet-Tolosan F–31326, France (C.B., M.Z., E.M., W.B., I.E., M.B., A.L., J.-C.P.); Fédération de Recherche 3450, Agrobiosciences, Interactions et Biodiversités, Plateforme Protéomique Génopole Toulouse Midi-Pyrénées, Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique, F–31077 Toulouse, France (M.R., C.P.); Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Toulouse F–31077, France (M.R., D.B., C.P.); and Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Depto. de Alimentos e Nutrição Experimental, 05508–000 São Paulo, Brazil (E.P.)
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