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Volumn 90, Issue , 2013, Pages 77-84

IsobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins

Author keywords

Bioinformatics; Computational proteomics; ITRAQ; Quantitative proteomics; Statistics; TMT

Indexed keywords

ARTICLE; COMPUTER PROGRAM; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM; STATISTICAL MODEL; ANIMAL; CHEMISTRY; HUMAN; PROTEIN DATABASE;

EID: 84882733620     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.02.022     Document Type: Article
Times cited : (19)

References (36)
  • 1
    • 2942564448 scopus 로고    scopus 로고
    • The RESID database of protein modifications as a resource and annotation tool
    • Garavelli J.S. The RESID database of protein modifications as a resource and annotation tool. Proteomics 2004, 4:1527-1533.
    • (2004) Proteomics , vol.4 , pp. 1527-1533
    • Garavelli, J.S.1
  • 2
    • 78650632764 scopus 로고    scopus 로고
    • Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast
    • Bodenmiller B., Wanka S., Kraft C., Urban J., Campbell D., Pedrioli P.G., et al. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal 2010, 3:rs4.
    • (2010) Sci Signal , vol.3
    • Bodenmiller, B.1    Wanka, S.2    Kraft, C.3    Urban, J.4    Campbell, D.5    Pedrioli, P.G.6
  • 3
    • 84863420067 scopus 로고    scopus 로고
    • Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium
    • van Noort V., Seebacher J., Bader S., Mohammed S., Vonkova I., Betts M.J., et al. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol 2012, 8:571.
    • (2012) Mol Syst Biol , vol.8 , pp. 571
    • van Noort, V.1    Seebacher, J.2    Bader, S.3    Mohammed, S.4    Vonkova, I.5    Betts, M.J.6
  • 4
    • 77954464041 scopus 로고    scopus 로고
    • Proteomics: a pragmatic perspective
    • Mallick P., Kuster B. Proteomics: a pragmatic perspective. Nat Biotechnol 2010, 28:695-709.
    • (2010) Nat Biotechnol , vol.28 , pp. 695-709
    • Mallick, P.1    Kuster, B.2
  • 5
    • 0037338365 scopus 로고    scopus 로고
    • Proteomic analysis of post-translational modifications
    • Mann M., Jensen O.N. Proteomic analysis of post-translational modifications. Nat Biotechnol 2003, 21:255-261.
    • (2003) Nat Biotechnol , vol.21 , pp. 255-261
    • Mann, M.1    Jensen, O.N.2
  • 6
    • 77956028057 scopus 로고    scopus 로고
    • Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics
    • Bodenmiller B., Aebersold R. Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics. Methods Enzymol 2010, 470:317-334.
    • (2010) Methods Enzymol , vol.470 , pp. 317-334
    • Bodenmiller, B.1    Aebersold, R.2
  • 7
    • 82455179484 scopus 로고    scopus 로고
    • Systematic and quantitative assessment of the ubiquitin-modified proteome
    • Kim W., Bennett E.J., Huttlin E.L., Guo A., Li J., Possemato A., et al. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell 2011, 44:325-340.
    • (2011) Mol Cell , vol.44 , pp. 325-340
    • Kim, W.1    Bennett, E.J.2    Huttlin, E.L.3    Guo, A.4    Li, J.5    Possemato, A.6
  • 8
    • 84869215170 scopus 로고    scopus 로고
    • Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae
    • Henriksen P., Wagner S.A., Weinert B.T., Sharma S., Bacinskaja G., Rehman M., et al. Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. Mol Cell Proteomics 2012, 11:1510-1522.
    • (2012) Mol Cell Proteomics , vol.11 , pp. 1510-1522
    • Henriksen, P.1    Wagner, S.A.2    Weinert, B.T.3    Sharma, S.4    Bacinskaja, G.5    Rehman, M.6
  • 9
    • 12444345515 scopus 로고    scopus 로고
    • Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
    • Thompson A., Schafer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 75:1895-1904.
    • (2003) Anal Chem , vol.75 , pp. 1895-1904
    • Thompson, A.1    Schafer, J.2    Kuhn, K.3    Kienle, S.4    Schwarz, J.5    Schmidt, G.6
  • 10
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
    • (2004) Mol Cell Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.N.2    Marchese, J.N.3    Williamson, B.4    Parker, K.5    Hattan, S.6
  • 11
    • 79958198057 scopus 로고    scopus 로고
    • General statistical modeling of data from protein relative expression isobaric tags
    • Breitwieser F.P., Muller A., Dayon L., Kocher T., Hainard A., Pichler P., et al. General statistical modeling of data from protein relative expression isobaric tags. J Proteome Res 2011, 10:2758-2766.
    • (2011) J Proteome Res , vol.10 , pp. 2758-2766
    • Breitwieser, F.P.1    Muller, A.2    Dayon, L.3    Kocher, T.4    Hainard, A.5    Pichler, P.6
  • 12
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins D.N., Pappin D.J., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 13
    • 0041358793 scopus 로고    scopus 로고
    • OLAV: towards high-throughput tandem mass spectrometry data identification
    • Colinge J., Masselot A., Giron M., Dessingy T., Magnin J. OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 2003, 3:1454-1463.
    • (2003) Proteomics , vol.3 , pp. 1454-1463
    • Colinge, J.1    Masselot, A.2    Giron, M.3    Dessingy, T.4    Magnin, J.5
  • 17
    • 82755182013 scopus 로고    scopus 로고
    • Universal and confident phosphorylation site localization using phosphoRS
    • Taus T., Kocher T., Pichler P., Paschke C., Schmidt A., Henrich C., et al. Universal and confident phosphorylation site localization using phosphoRS. J Proteome Res 2011, 10:5354-5362.
    • (2011) J Proteome Res , vol.10 , pp. 5354-5362
    • Taus, T.1    Kocher, T.2    Pichler, P.3    Paschke, C.4    Schmidt, A.5    Henrich, C.6
  • 19
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: open source software for rapid proteomics tools development
    • Kessner D., Chambers M., Burke R., Agus D., Mallick P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24:2534-2536.
    • (2008) Bioinformatics , vol.24 , pp. 2534-2536
    • Kessner, D.1    Chambers, M.2    Burke, R.3    Agus, D.4    Mallick, P.5
  • 21
    • 84860879590 scopus 로고    scopus 로고
    • Modification site localization scoring: strategies and performance
    • Chalkley R.J., Clauser K.R. Modification site localization scoring: strategies and performance. Mol Cell Proteomics 2012, 11:3-14.
    • (2012) Mol Cell Proteomics , vol.11 , pp. 3-14
    • Chalkley, R.J.1    Clauser, K.R.2
  • 24
    • 33749853607 scopus 로고    scopus 로고
    • A probability-based approach for high-throughput protein phosphorylation analysis and site localization
    • Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 2006, 24:1285-1292.
    • (2006) Nat Biotechnol , vol.24 , pp. 1285-1292
    • Beausoleil, S.A.1    Villen, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 25
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127:635-648.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4    Kumar, C.5    Mortensen, P.6
  • 26
    • 51649090664 scopus 로고    scopus 로고
    • PhosphoScore: an open-source phosphorylation site assignment tool for MSn data
    • Ruttenberg B.E., Pisitkun T., Knepper M.A., Hoffert J.D. PhosphoScore: an open-source phosphorylation site assignment tool for MSn data. J Proteome Res 2008, 7:3054-3059.
    • (2008) J Proteome Res , vol.7 , pp. 3054-3059
    • Ruttenberg, B.E.1    Pisitkun, T.2    Knepper, M.A.3    Hoffert, J.D.4
  • 27
    • 59049086847 scopus 로고    scopus 로고
    • Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry
    • Swaney D.L., Wenger C.D., Thomson J.A., Coon J.J. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A 2009, 106:995-1000.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 995-1000
    • Swaney, D.L.1    Wenger, C.D.2    Thomson, J.A.3    Coon, J.J.4
  • 28
    • 79961013401 scopus 로고    scopus 로고
    • Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes
    • 009654
    • Wu R., Dephoure N., Haas W., Huttlin E.L., Zhai B., Sowa M.E., et al. Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Mol Cell Proteomics 2011, 10(8):M111. 009654.
    • (2011) Mol Cell Proteomics , vol.10 , Issue.8
    • Wu, R.1    Dephoure, N.2    Haas, W.3    Huttlin, E.L.4    Zhai, B.5    Sowa, M.E.6
  • 29
    • 84857047339 scopus 로고    scopus 로고
    • PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    • Hornbeck P.V., Kornhauser J.M., Tkachev S., Zhang B., Skrzypek E., Murray B., et al. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res 2012, 40:D261-D270.
    • (2012) Nucleic Acids Res , vol.40
    • Hornbeck, P.V.1    Kornhauser, J.M.2    Tkachev, S.3    Zhang, B.4    Skrzypek, E.5    Murray, B.6
  • 30
    • 70349974261 scopus 로고    scopus 로고
    • High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all
    • Kocher T., Pichler P., Schutzbier M., Stingl C., Kaul A., Teucher N., et al. High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all. J Proteome Res 2009, 8:4743-4752.
    • (2009) J Proteome Res , vol.8 , pp. 4743-4752
    • Kocher, T.1    Pichler, P.2    Schutzbier, M.3    Stingl, C.4    Kaul, A.5    Teucher, N.6
  • 31
    • 79955831978 scopus 로고    scopus 로고
    • Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos
    • Frese C.K., Altelaar A.F., Hennrich M.L., Nolting D., Zeller M., Griep-Raming J., et al. Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. J Proteome Res 2011, 10:2377-2388.
    • (2011) J Proteome Res , vol.10 , pp. 2377-2388
    • Frese, C.K.1    Altelaar, A.F.2    Hennrich, M.L.3    Nolting, D.4    Zeller, M.5    Griep-Raming, J.6
  • 32
    • 79952306399 scopus 로고    scopus 로고
    • COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA
    • Wenger C.D., Phanstiel D.H., Lee M.V., Bailey D.J., Coon J.J. COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. Proteomics 2011, 11:1064-1074.
    • (2011) Proteomics , vol.11 , pp. 1064-1074
    • Wenger, C.D.1    Phanstiel, D.H.2    Lee, M.V.3    Bailey, D.J.4    Coon, J.J.5
  • 34
    • 79958696694 scopus 로고    scopus 로고
    • The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling
    • Hsu P.P., Kang S.A., Rameseder J., Zhang Y., Ottina K.A., Lim D., et al. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science 2011, 332:1317-1322.
    • (2011) Science , vol.332 , pp. 1317-1322
    • Hsu, P.P.1    Kang, S.A.2    Rameseder, J.3    Zhang, Y.4    Ottina, K.A.5    Lim, D.6
  • 36
    • 84872387673 scopus 로고    scopus 로고
    • EasyProt - an easy-to-use graphical platform for proteomics data analysis
    • Gluck F., Hoogland C., Antinori P., Robin X., Nikitin F., Zufferey A., et al. EasyProt - an easy-to-use graphical platform for proteomics data analysis. J Proteomics 2012, 79C:146-160.
    • (2012) J Proteomics , vol.79 C , pp. 146-160
    • Gluck, F.1    Hoogland, C.2    Antinori, P.3    Robin, X.4    Nikitin, F.5    Zufferey, A.6


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