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Volumn 15, Issue 2, 2016, Pages 703-714

MASH suite pro: A comprehensive software tool for top-down proteomics

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DRUG MIXTURE; GENETIC VARIABILITY; MASS SPECTROMETRY; MOLECULAR WEIGHT; NONHUMAN; PORCINE MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; ALGORITHM; GENETICS; PROCEDURES; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84957900751     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O115.054387     Document Type: Article
Times cited : (113)

References (53)
  • 2
    • 79959424627 scopus 로고    scopus 로고
    • Quantitative, high-resolution proteomics for data-driven systems biology
    • Cox, J., and Mann, M. (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annu. Rev. Biochem. 80, 273-299
    • (2011) Annu. Rev. Biochem , vol.80 , pp. 273-299
    • Cox, J.1    Mann, M.2
  • 3
    • 84929129370 scopus 로고    scopus 로고
    • Multidimensional proteomics for cell biology
    • Larance, M., and Lamond, A. I. (2015) Multidimensional proteomics for cell biology. Nat. Rev. Mol. Cell Biol. 16, 269-280
    • (2015) Nat. Rev. Mol. Cell Biol , vol.16 , pp. 269-280
    • Larance, M.1    Lamond, A.I.2
  • 4
    • 84861897793 scopus 로고    scopus 로고
    • Mass spectrometrybased proteomics and network biology
    • Bensimon, A., Heck, A. J., and Aebersold, R. (2012) Mass spectrometrybased proteomics and network biology. Annu. Rev. Biochem. 81, 379-405
    • (2012) Annu. Rev. Biochem , vol.81 , pp. 379-405
    • Bensimon, A.1    Heck, A.J.2    Aebersold, R.3
  • 5
    • 67651173106 scopus 로고    scopus 로고
    • Proteomics by mass spectrometry: Approaches, advances, and applications
    • Yates, J. R., Ruse, C. I., and Nakorchevsky, A. (2009) Proteomics by mass spectrometry: Approaches, advances, and applications. Annu. Rev. Biomed. Eng. 11, 49-79
    • (2009) Annu. Rev. Biomed. Eng , vol.11 , pp. 49-79
    • Yates, J.R.1    Ruse, C.I.2    Nakorchevsky, A.3
  • 6
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii, A. I., Vitek, O., and Aebersold, R. (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4, 787-797
    • (2007) Nat. Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 7
    • 37249014081 scopus 로고    scopus 로고
    • The biological impact of mass-spectrometry-based proteomics
    • Cravatt, B. F., Simon, G. M., and Yates, J. R., 3rd (2007) The biological impact of mass-spectrometry-based proteomics. Nature 450, 991-1000
    • (2007) Nature , vol.450 , pp. 991-1000
    • Cravatt, B.F.1    Simon, G.M.2    Yates, J.R.3
  • 8
    • 52049083485 scopus 로고    scopus 로고
    • Phosphoproteomics: Unraveling the signaling web
    • Huang, P. H., and White, F. M. (2008) Phosphoproteomics: Unraveling the signaling web. Mol. Cell 31, 777-781
    • (2008) Mol. Cell , vol.31 , pp. 777-781
    • Huang, P.H.1    White, F.M.2
  • 9
    • 84891790963 scopus 로고    scopus 로고
    • A proteomic perspective of Sirtuin 6 (SIRT6) phosphorylation and interactions and their dependence on its catalytic activity
    • Miteva, Y. V., and Cristea, I. M. (2014) A proteomic perspective of Sirtuin 6 (SIRT6) phosphorylation and interactions and their dependence on its catalytic activity. Mol. Cell. Proteomics 13, 168-183
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 168-183
    • Miteva, Y.V.1    Cristea, I.M.2
  • 10
    • 33749615256 scopus 로고    scopus 로고
    • Chemistry. Mass spectrometry: Bottom-up or top-down?
    • Chait, B. T. (2006) Chemistry. Mass spectrometry: Bottom-up or top-down? Science 314, 65-66
    • (2006) Science , vol.314 , pp. 65-66
    • Chait, B.T.1
  • 11
    • 84874625369 scopus 로고    scopus 로고
    • Proteoform: A single term describing protein complexity
    • Smith, L. M., Kelleher, N. L., and Proteomics, C. f. T. D. (2013) Proteoform: A single term describing protein complexity. Nat Methods 10, 186-187
    • (2013) Nat Methods , vol.10 , pp. 186-187
    • Smith, L.M.1    Kelleher, N.L.2    Proteomics, C.F.T.D.3
  • 12
    • 35848949043 scopus 로고    scopus 로고
    • Decoding protein modifications using top-down mass spectrometry
    • Siuti, N., and Kelleher, N. L. (2007) Decoding protein modifications using top-down mass spectrometry. Nat Methods 4, 817-821
    • (2007) Nat Methods , vol.4 , pp. 817-821
    • Siuti, N.1    Kelleher, N.L.2
  • 13
    • 84899827440 scopus 로고    scopus 로고
    • Top-down proteomics in health and disease: Challenges and opportunities
    • Gregorich, Z. R., and Ge, Y. (2014) Top-down proteomics in health and disease: Challenges and opportunities. Proteomics 14, 1195-1210
    • (2014) Proteomics , vol.14 , pp. 1195-1210
    • Gregorich, Z.R.1    Ge, Y.2
  • 17
    • 84859393607 scopus 로고    scopus 로고
    • Comprehensive analysis of protein modifications by top-down mass spectrometry
    • Zhang, H., and Ge, Y. (2011) Comprehensive analysis of protein modifications by top-down mass spectrometry. Circ. Cardiovasc. Genet. 4, 711
    • (2011) Circ. Cardiovasc. Genet , vol.4 , pp. 711
    • Zhang, H.1    Ge, Y.2
  • 20
    • 84876114159 scopus 로고    scopus 로고
    • Intact protein mass spectrometry and top-down proteomics
    • Whitelegge, J. (2013) Intact protein mass spectrometry and top-down proteomics. Expert Rev. Proteomics 10, 127-129
    • (2013) Expert Rev. Proteomics , vol.10 , pp. 127-129
    • Whitelegge, J.1
  • 25
    • 0034582319 scopus 로고    scopus 로고
    • Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules
    • Horn, D. M., Zubarev, R. A., and McLafferty, F. W. (2000) Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 11, 320-332
    • (2000) J. Am. Soc. Mass Spectrom , vol.11 , pp. 320-332
    • Horn, D.M.1    Zubarev, R.A.2    McLafferty, F.W.3
  • 27
    • 84928344005 scopus 로고    scopus 로고
    • Bayesian deconvolution of mass and ion mobility spectra: From binary interactions to polydisperse ensembles
    • Marty, M. T., Baldwin, A. J., Marklund, E. G., Hochberg, G. K., Benesch, J. L., and Robinson, C. V. (2015) Bayesian deconvolution of mass and ion mobility spectra: From binary interactions to polydisperse ensembles. Anal. Chem. 87, 4370-4376
    • (2015) Anal. Chem , vol.87 , pp. 4370-4376
    • Marty, M.T.1    Baldwin, A.J.2    Marklund, E.G.3    Hochberg, G.K.4    Benesch, J.L.5    Robinson, C.V.6
  • 28
    • 3242887156 scopus 로고    scopus 로고
    • ProSight PTM: An integrated environment for protein identification and characterization by top-down mass spectrometry
    • LeDuc, R. D., Taylor, G. K., Kim, Y. B., Januszyk, T. E., Bynum, L. H., Sola, J. V., Garavelli, J. S., and Kelleher, N. L. (2004) ProSight PTM: An integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res. 32, W340-W345
    • (2004) Nucleic Acids Res , vol.32 , pp. W340-W345
    • LeDuc, R.D.1    Taylor, G.K.2    Kim, Y.B.3    Januszyk, T.E.4    Bynum, L.H.5    Sola, J.V.6    Garavelli, J.S.7    Kelleher, N.L.8
  • 30
    • 66149096321 scopus 로고    scopus 로고
    • Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry
    • Karabacak, N. M., Li, L., Tiwari, A., Hayward, L. J., Hong, P., Easterling, M. L., and Agar, J. N. (2009) Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry. Mol. Cell. Proteomics 8, 846-856
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 846-856
    • Karabacak, N.M.1    Li, L.2    Tiwari, A.3    Hayward, L.J.4    Hong, P.5    Easterling, M.L.6    Agar, J.N.7
  • 33
    • 1642272372 scopus 로고    scopus 로고
    • Shotgun annotation of histone modifications: A new approach for streamlined characterization of proteins by top down mass spectrometry
    • Pesavento, J. J., Kim, Y. B., Taylor, G. K., and Kelleher, N. L. (2004) Shotgun annotation of histone modifications: A new approach for streamlined characterization of proteins by top down mass spectrometry. J. Am. Chem. Soc. 126, 3386-3387
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 3386-3387
    • Pesavento, J.J.1    Kim, Y.B.2    Taylor, G.K.3    Kelleher, N.L.4
  • 34
    • 81555226888 scopus 로고    scopus 로고
    • An algorithm for identifying multiply modified endogenous proteins using both full-scan and high-resolution tandem mass spectrometric data
    • Mazur, M. T., and Fyhr, R. (2011) An algorithm for identifying multiply modified endogenous proteins using both full-scan and high-resolution tandem mass spectrometric data. Rapid Commun. Mass Spectrom. 25, 3617-3626
    • (2011) Rapid Commun. Mass Spectrom , vol.25 , pp. 3617-3626
    • Mazur, M.T.1    Fyhr, R.2
  • 35
    • 0034915775 scopus 로고    scopus 로고
    • Mutation-Tolerant protein identification by mass spectrometry
    • Pevzner, P. A., Dancík, V., and Tang, C. L. (2000) Mutation-Tolerant protein identification by mass spectrometry. J. Comput. Biol. 7, 777-787
    • (2000) J. Comput. Biol , vol.7 , pp. 777-787
    • Pevzner, P.A.1    Dancík, V.2    Tang, C.L.3
  • 36
    • 84894470909 scopus 로고    scopus 로고
    • MASH Suite: A user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization
    • Guner, H., Close, P. L., Cai, W., Zhang, H., Peng, Y., Gregorich, Z. R., and Ge, Y. (2014) MASH Suite: A user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization. J. Am. Soc. Mass Spectrom. 25, 464-470
    • (2014) J. Am. Soc. Mass Spectrom , vol.25 , pp. 464-470
    • Guner, H.1    Close, P.L.2    Cai, W.3    Zhang, H.4    Peng, Y.5    Gregorich, Z.R.6    Ge, Y.7
  • 38
    • 62149121444 scopus 로고    scopus 로고
    • Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data
    • Jaitly, N., Mayampurath, A., Littlefield, K., Adkins, J. N., Anderson, G. A., and Smith, R. D. (2009) Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics 10, 87
    • (2009) BMC Bioinformatics , vol.10 , pp. 87
    • Jaitly, N.1    Mayampurath, A.2    Littlefield, K.3    Adkins, J.N.4    Anderson, G.A.5    Smith, R.D.6
  • 39
    • 84929590920 scopus 로고    scopus 로고
    • Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics
    • Valeja, S. G., Xiu, L., Gregorich, Z. R., Guner, H., Jin, S., and Ge, Y. (2015) Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Anal. Chem. 87, 5363-5371
    • (2015) Anal. Chem , vol.87 , pp. 5363-5371
    • Valeja, S.G.1    Xiu, L.2    Gregorich, Z.R.3    Guner, H.4    Jin, S.5    Ge, Y.6
  • 40
  • 42
    • 84906058717 scopus 로고    scopus 로고
    • Top-down mass spectrometry of cardiac myofilament proteins in health and disease
    • Peng, Y., Ayaz-Guner, S., Yu, D., and Ge, Y. (2014) Top-down mass spectrometry of cardiac myofilament proteins in health and disease. Proteomics Clin. Appl. 8, 554-568
    • (2014) Proteomics Clin. Appl , vol.8 , pp. 554-568
    • Peng, Y.1    Ayaz-Guner, S.2    Yu, D.3    Ge, Y.4
  • 43
    • 69149100342 scopus 로고    scopus 로고
    • Top-down highresolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state
    • Ge, Y., Rybakova, I. N., Xu, Q., and Moss, R. L. (2009) Top-down highresolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state. Proc. Natl. Acad. Sci. U.S.A. 106, 12658-12663
    • (2009) Proc. Natl. Acad. Sci. U.S.A , vol.106 , pp. 12658-12663
    • Ge, Y.1    Rybakova, I.N.2    Xu, Q.3    Moss, R.L.4
  • 46
    • 84905680598 scopus 로고    scopus 로고
    • Effective protein separation by coupling hydrophobic interaction and reverse phase chromatography for top-down proteomics
    • Xiu, L., Valeja, S. G., Alpert, A. J., Jin, S., and Ge, Y. (2014) Effective protein separation by coupling hydrophobic interaction and reverse phase chromatography for top-down proteomics. Anal. Chem. 86, 7899-7906
    • (2014) Anal. Chem , vol.86 , pp. 7899-7906
    • Xiu, L.1    Valeja, S.G.2    Alpert, A.J.3    Jin, S.4    Ge, Y.5
  • 47
    • 84923557164 scopus 로고    scopus 로고
    • Specific enrichment of phosphoproteins using functionalized multivalent nanoparticles
    • Hwang, L., Ayaz-Guner, S., Gregorich, Z. R., Cai, W., Valeja, S. G., Jin, S., and Ge, Y. (2015) Specific enrichment of phosphoproteins using functionalized multivalent nanoparticles. J. Am. Chem. Soc. 137, 2432-2435
    • (2015) J. Am. Chem. Soc , vol.137 , pp. 2432-2435
    • Hwang, L.1    Ayaz-Guner, S.2    Gregorich, Z.R.3    Cai, W.4    Valeja, S.G.5    Jin, S.6    Ge, Y.7
  • 48
    • 58149209843 scopus 로고
    • Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions
    • Senko, M. W., Beu, S. C., and McLaffertycor, F. W. (1995) Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 6, 229-233
    • (1995) J. Am. Soc. Mass Spectrom , vol.6 , pp. 229-233
    • Senko, M.W.1    Beu, S.C.2    McLaffertycor, F.W.3
  • 52
    • 2442624720 scopus 로고    scopus 로고
    • Monomeric Cu, Zn-superoxide dismutase is a common misfolding intermediate in the oxidation models of sporadic and familial amyotrophic lateral sclerosis
    • Rakhit, R., Crow, J. P., Lepock, J. R., Kondejewski, L. H., Cashman, N. R., and Chakrabartty, A. (2004) Monomeric Cu, Zn-superoxide dismutase is a common misfolding intermediate in the oxidation models of sporadic and familial amyotrophic lateral sclerosis. J. Biol. Chem. 279, 15499-15504
    • (2004) J. Biol. Chem , vol.279 , pp. 15499-15504
    • Rakhit, R.1    Crow, J.P.2    Lepock, J.R.3    Kondejewski, L.H.4    Cashman, N.R.5    Chakrabartty, A.6


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