메뉴 건너뛰기




Volumn 3, Issue SEP, 2012, Pages

Non-biased enrichment does not improve quantitative proteomic delineation of reovirus T3D-infected HeLa cell protein alterations

Author keywords

Bioinformatics; Host cell alterations; Liquid chromatography; Mass spectrometry; RNA virus; Virus infection

Indexed keywords


EID: 84875795470     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2012.00310     Document Type: Article
Times cited : (7)

References (41)
  • 2
    • 68949188073 scopus 로고    scopus 로고
    • Mammalian reoviruses: propagation, quantification, and storage
    • Chapter 15 Unit15C
    • Berard, A., and Coombs, K. M. (2009). Mammalian reoviruses: propagation, quantification, and storage. Curr. Protoc. Microbiol. Chapter 15, Unit15C.1.
    • (2009) Curr. Protoc. Microbiol. , pp. 1
    • Berard, A.1    Coombs, K.M.2
  • 3
    • 17444392125 scopus 로고    scopus 로고
    • Application of isotope coded affinity tag (ICAT) analysis for the identification of differentially expressed proteins following infection of Atlantic salmon (Salmo salar) with infectious hematopoi-etic necrosis virus (IHNV) or Reni-bacterium salmoninarum (BKD)
    • Booy, A. T., Haddow, J. D., Ohlund, L. B., Hardie, D. B., and Olafson, R. W. (2005). Application of isotope coded affinity tag (ICAT) analysis for the identification of differentially expressed proteins following infection of Atlantic salmon (Salmo salar) with infectious hematopoi-etic necrosis virus (IHNV) or Reni-bacterium salmoninarum (BKD). J. Proteome Res. 4, 325-334.
    • (2005) J. Proteome Res. , vol.4 , pp. 325-334
    • Booy, A.T.1    Haddow, J.D.2    Ohlund, L.B.3    Hardie, D.B.4    Olafson, R.W.5
  • 5
    • 0032515141 scopus 로고    scopus 로고
    • Reovirus therapy of tumors with activated Ras pathway
    • Coffey, M. C., Strong, J. E., Forsyth, P. A., and Lee, P. W. (1998). Reovirus therapy of tumors with activated Ras pathway. Science 282, 1332-1334.
    • (1998) Science , vol.282 , pp. 1332-1334
    • Coffey, M.C.1    Strong, J.E.2    Forsyth, P.A.3    Lee, P.W.4
  • 6
    • 80054732682 scopus 로고    scopus 로고
    • Quantitative proteomics of complex mixtures
    • Coombs, K. M. (2011). Quantitative proteomics of complex mixtures. Expert Rev. Proteomics 8, 659-677.
    • (2011) Expert Rev. Proteomics , vol.8 , pp. 659-677
    • Coombs, K.M.1
  • 8
    • 0041707779 scopus 로고    scopus 로고
    • Reovirus-induced alteration in expression of apoptosis and DNA repair genes with potential roles in viral pathogenesis
    • DeBiasi, R. L., Clarke, P., Meintzer, S., Jotte, R., Kleinschmidt-Demasters, B K., Johnson, G. L., and Tyler, K.L. (2003). Reovirus-induced alteration in expression of apoptosis and DNA repair genes with potential roles in viral pathogenesis. J. Virol. 77, 8934-8947.
    • (2003) J. Virol. , vol.77 , pp. 8934-8947
    • DeBiasi, R.L.1    Clarke, P.2    Meintzer, S.3    Jotte, R.4    Kleinschmidt-Demasters, B.K.5    Johnson, G.L.6    Tyler, K.L.7
  • 9
    • 0038005018 scopus 로고    scopus 로고
    • DAVID: Database for annotation, visualization, and integrated discovery
    • doi: 10.1186/gb-2003-4-9-r60
    • Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., and Lempicki, R. A. (2003). DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol. 4. doi: 10.1186/gb-2003-4-9-r60
    • (2003) Genome Biol. , vol.4
    • Dennis, G.1    Sherman, B.T.2    Hosack, D.A.3    Yang, J.4    Gao, W.5    Lane, H.C.6    Lempicki, R.A.7
  • 11
    • 51949083217 scopus 로고    scopus 로고
    • Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics
    • Dwivedi, R. C., Spicer, V., Harder, M., Antonovici, M., Ens, W., Standing, K. G., Wilkins, J. A., and Krokhin, O. V. (2008). Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal. Chem. 80, 7036-7042.
    • (2008) Anal. Chem. , vol.80 , pp. 7036-7042
    • Dwivedi, R.C.1    Spicer, V.2    Harder, M.3    Antonovici, M.4    Ens, W.5    Standing, K.G.6    Wilkins, J.A.7    Krokhin, O.V.8
  • 13
    • 84857938446 scopus 로고    scopus 로고
    • Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
    • PMID: 22278370.[Epub ahead of print]
    • Geiger, T., Wehner, A., Schaab, C., Cox, J., and Mann M. (2012). Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol. Cell. Proteomics. PMID: 22278370. [Epub ahead of print].
    • (2012) Mol. Cell. Proteomics.
    • Geiger, T.1    Wehner, A.2    Schaab, C.3    Cox, J.4    Mann, M.5
  • 14
    • 0036678864 scopus 로고    scopus 로고
    • Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza
    • Geiss, G. K., Salvatore, M., Tumpey, T. M., Carter, V. S., Wang, X. Y., Basler, C F., Taubenberger, J. K., Bumgar-ner, R. E., Palese, P., Katze, M. G., and Garcia-Sastre, A. (2002). Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza. Proc. Natl. Acad. Sci. U.S.A. 99, 10736-10741.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 10736-10741
    • Geiss, G.K.1    Salvatore, M.2    Tumpey, T.M.3    Carter, V.S.4    Wang, X.Y.5    Basler, C.F.6    Taubenberger, J.K.7    Bumgar-ner, R.E.8    Palese, P.9    Katze, M.G.10    Garcia-Sastre, A.11
  • 15
    • 26444539668 scopus 로고    scopus 로고
    • Orthogonality of separation in two-dimensional liquid chromatography
    • Gilar, M., Olivova, P., Daly, A. E., and Gebler, J. C. (2005). Orthogonality of separation in two-dimensional liquid chromatography. Anal. Chem. 77, 6426-6434.
    • (2005) Anal. Chem. , vol.77 , pp. 6426-6434
    • Gilar, M.1    Olivova, P.2    Daly, A.E.3    Gebler, J.C.4
  • 16
    • 33847047461 scopus 로고    scopus 로고
    • Epigenetics: a landscape takes shape
    • Goldberg, A. D., Allis, C. D., and Bernstein, E. (2007). Epigenetics: a landscape takes shape. Cell 128,635-638.
    • (2007) Cell , vol.128 , pp. 635-638
    • Goldberg, A.D.1    Allis, C.D.2    Bernstein, E.3
  • 17
    • 34548649449 scopus 로고    scopus 로고
    • JAK-STAT signaling pathways are activated in the brain following reovirus infection
    • Goody, R. J., Beckham, J. D., Rubtsova, K., and Tyler, K. L. (2007). JAK-STAT signaling pathways are activated in the brain following reovirus infection.J. Neurovirol. 13, 373-383.
    • (2007) J. Neurovirol. , vol.13 , pp. 373-383
    • Goody, R.J.1    Beckham, J.D.2    Rubtsova, K.3    Tyler, K.L.4
  • 18
    • 0036788192 scopus 로고    scopus 로고
    • Interferon-induced mx proteins: dynamin-like GTPases with antiviral activity
    • Haller, O., and Kochs, G. (2002). Interferon-induced mx proteins: dynamin-like GTPases with antiviral activity. Traffic 3, 710-717.
    • (2002) Traffic , vol.3 , pp. 710-717
    • Haller, O.1    Kochs, G.2
  • 19
    • 68149098653 scopus 로고    scopus 로고
    • Protective role of interferon-induced Mx GTPases against influenza viruses
    • Haller, O., Staeheli, P., and Kochs, G. (2009). Protective role of interferon-induced Mx GTPases against influenza viruses. Rev. Sci. Tech. 28, 219-231.
    • (2009) Rev. Sci. Tech. , vol.28 , pp. 219-231
    • Haller, O.1    Staeheli, P.2    Kochs, G.3
  • 20
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009a). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4,44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 21
    • 68949160963 scopus 로고    scopus 로고
    • Global proteome analysis of hepatitis B virus expressing human hepatoblastoma cell line HepG2
    • Huang, Q. L., Wang, L., Bai, S. Y., Lin, W. S., Chen, W. N., Lin, J. Y., and Lin, X. (2009b). Global proteome analysis of hepatitis B virus expressing human hepatoblastoma cell line HepG2.J. Med. Virol. 81,1539-1550.
    • (2009) J. Med. Virol. , vol.81 , pp. 1539-1550
    • Huang, Q.L.1    Wang, L.2    Bai, S.Y.3    Lin, W.S.4    Chen, W.N.5    Lin, J.Y.6    Lin, X.7
  • 22
    • 36049046122 scopus 로고    scopus 로고
    • An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularen-sis
    • Jiang, J., Parker, C. E., Fuller, J. R., Kawula, T. H., and Borchers, C. H. (2007). An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularen-sis. Anal. Chim. Acta 605, 70-79.
    • (2007) Anal. Chim. Acta , vol.605 , pp. 70-79
    • Jiang, J.1    Parker, C.E.2    Fuller, J.R.3    Kawula, T.H.4    Borchers, C.H.5
  • 23
    • 60849087975 scopus 로고    scopus 로고
    • Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition
    • Keshamouni, V G., Jagtap, P., Michai-lidis, G., Strahler, J. R., Kuick, R., Reka, A. K., Papoulias, P., Krish-napuram, R., Srirangam, A., Stan-diford, T. J., Andrews, P. C., and Omenn, G. S. (2009). Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition. J. Proteome Res. 8, 35-47.
    • (2009) J. Proteome Res. , vol.8 , pp. 35-47
    • Keshamouni, V.G.1    Jagtap, P.2    Michai-lidis, G.3    Strahler, J.R.4    Kuick, R.5    Reka, A.K.6    Papoulias, P.7    Krish-napuram, R.8    Srirangam, A.9    Stan-diford, T.J.10    Andrews, P.C.11    Omenn, G.S.12
  • 26
    • 0033818477 scopus 로고    scopus 로고
    • A comparative analysis of freon substitutes in the purification of reovirus and calicivirus
    • Mendez, II, Hermann, L. L., Hazel-ton, P. R., and Coombs, K. M. (2000). A comparative analysis of freon substitutes in the purification of reovirus and calicivirus. J. Virol. Methods 90, 59-67.
    • (2000) J. Virol. Methods , vol.90 , pp. 59-67
    • Mendez, I.I.1    Hermann, L.L.2    Hazel-ton, P.R.3    Coombs, K.M.4
  • 27
    • 84860403975 scopus 로고    scopus 로고
    • Stabilisation of p53 enhances reovirus-induced apoptosis and virus spread through p53-dependent NF-kappa B activation
    • Pan, D., Pan, L. Z., Hill, R., Marcato, P., Shmulevitz, M., Vassilev, L. T., and Lee, P. W K. (2011). Stabilisation of p53 enhances reovirus-induced apoptosis and virus spread through p53-dependent NF-kappa B activation. Br. J. Cancer 105, 1012-1022.
    • (2011) Br. J. Cancer , vol.105 , pp. 1012-1022
    • Pan, D.1    Pan, L.Z.2    Hill, R.3    Marcato, P.4    Shmulevitz, M.5    Vassilev, L.T.6    Lee, P.W.K.7
  • 29
    • 34548650332 scopus 로고    scopus 로고
    • Orthoreoviruses and their replication
    • eds D. M. Knipe and P. M. Howley (Philadelphia: Lippincott Williams &Wilkins)
    • Schiff, L. A., Nibert, M. L., and Tyler, K. L. (2007). Orthoreoviruses and their replication, in Fields Virology, Vol. 5, eds D. M. Knipe and P. M. Howley (Philadelphia: Lippincott Williams &Wilkins), 1853-1915.
    • (2007) Fields Virology , vol.5 , pp. 1853-1915
    • Schiff, L.A.1    Nibert, M.L.2    Tyler, K.L.3
  • 30
    • 70349234222 scopus 로고    scopus 로고
    • Rotavirus and reovirus modulation of the interferon response
    • Sherry, B. (2009). Rotavirus and reovirus modulation of the interferon response. J. Interferon Cytokine Res. 29, 559-567.
    • (2009) J. Interferon Cytokine Res. , pp. 559-567
    • Sherry, B.1
  • 31
    • 52649090784 scopus 로고    scopus 로고
    • Quantitative whole-cell proteome analysis of pseudorabies virus-infected cells
    • Skiba, M., Mettenleiter, T. C., and Karger, A. (2008). Quantitative whole-cell proteome analysis of pseudorabies virus-infected cells. J. Virol. 82, 9689-9699.
    • (2008) J. Virol , vol.82 , pp. 9689-9699
    • Skiba, M.1    Mettenleiter, T.C.2    Karger, A.3
  • 32
    • 0014627613 scopus 로고
    • Polypeptide components of virions, top component and cores of reovirus type 3
    • Smith, R. E., Zweerink, H. J., and Joklik, W K. (1969). Polypeptide components of virions, top component and cores of reovirus type 3. Virology 39, 791-810.
    • (1969) Virology , vol.39 , pp. 791-810
    • Smith, R.E.1    Zweerink, H.J.2    Joklik, W.K.3
  • 33
    • 36448943278 scopus 로고    scopus 로고
    • Sequence-specific retention calculator
    • A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns.
    • Spicer, V., Yamchuk, A., Cortens, J., Sousa, S., Ens, W., Standing, K. G., Wilkins, J. A., and Krokhin, O. (2007). Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns. Anal. Chem. 79, 8762-8768.
    • (2007) Anal. Chem. , vol.79 , pp. 8762-8768
    • Spicer, V.1    Yamchuk, A.2    Cortens, J.3    Sousa, S.4    Ens, W.5    Standing, K.G.6    Wilkins, J.A.7    Krokhin, O.8
  • 34
    • 33645463240 scopus 로고    scopus 로고
    • Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels
    • Stewart, J. J., White, J. T.,Yan,X., Collins, S., Drescher, C. W., Urban, N. D., Hood, L., and Lin, B. (2006). Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels. Mol. Cell Proteomics 5, 433-443.
    • (2006) Mol. Cell Proteomics , vol.5 , pp. 433-443
    • Stewart, J.J.1    White, J.T.2    Yan, X.3    Collins, S.4    Drescher, C.W.5    Urban, N.D.6    Hood, L.7    Lin, B.8
  • 37
    • 84875823125 scopus 로고    scopus 로고
    • Reoviruses
    • doi: 10.1038/npg.els.0004289, (Elsevier)
    • Tran, A. T., and Coombs, K. M. (2006).Reoviruses,in Encyclopedia ofLifeSciences,Vol. 2. (Elsevier). doi: 10.1038/npg.els.0004289
    • (2006) Encyclopedia ofLifeSciences , vol.2
    • Tran, A.T.1    Coombs, K.M.2
  • 38
    • 67650713700 scopus 로고    scopus 로고
    • Quantitative analysis of cellular proteome alterations in human influenza A virus-infected mammalian cell lines
    • Vester, D., Rapp, E., Gade, D., Genzel, Y., and Reichl, U. (2009). Quantitative analysis of cellular proteome alterations in human influenza A virus-infected mammalian cell lines. Proteomics 9, 3316-3327.
    • (2009) Proteomics , vol.9 , pp. 3316-3327
    • Vester, D.1    Rapp, E.2    Gade, D.3    Genzel, Y.4    Reichl, U.5
  • 39
    • 66449095920 scopus 로고    scopus 로고
    • Protein profile in hepatitis B virus replicating rat primary hepatocytes and HepG2 cells by iTRAQ-coupled 2-D LC-MS/MS analysis: insights on liver angiogenesis
    • Zhang, J., Niu, D., Sui, J., Ching, C. B., and Chen, W N. (2009). Protein profile in hepatitis B virus replicating rat primary hepatocytes and HepG2 cells by iTRAQ-coupled 2-D LC-MS/MS analysis: insights on liver angiogenesis. Proteomics 9, 2836-2845.
    • (2009) Proteomics , vol.9 , pp. 2836-2845
    • Zhang, J.1    Niu, D.2    Sui, J.3    Ching, C.B.4    Chen, W.N.5
  • 40
    • 41949132839 scopus 로고    scopus 로고
    • Combination of affinity depletion of abundant proteins and reversed-phase fractionation in proteomic analysis of human plasma/serum
    • Zolotarjova, N., Mrozinski, P., Chen, H., and Martosella, J. (2008). Combination of affinity depletion of abundant proteins and reversed-phase fractionation in proteomic analysis of human plasma/serum. J. Chro-matogr.A 1189,332-338.
    • (2008) J. Chro-matogr.A , vol.1189 , pp. 332-338
    • Zolotarjova, N.1    Mrozinski, P.2    Chen, H.3    Martosella, J.4
  • 41
    • 60049100923 scopus 로고    scopus 로고
    • Reovirus mu2 protein inhibits interferon signaling through a novel mechanism involving nuclear accumulation of interferon regulatory factor 9
    • Zurney, J., Kobayashi, T., Holm, G. H., Dermody, T. S., and Sherry, B. (2009). Reovirus mu2 protein inhibits interferon signaling through a novel mechanism involving nuclear accumulation of interferon regulatory factor 9. J. Virol. 83, 2178-2187.
    • (2009) J. Virol , vol.83 , pp. 2178-2187
    • Zurney, J.1    Kobayashi, T.2    Holm, G.H.3    Dermody, T.S.4    Sherry, B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.