메뉴 건너뛰기




Volumn 5, Issue 10, 2006, Pages 1927-1941

PEPPeR, a platform for experimental proteomic pattern recognition

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA CASEIN; APROTININ; BETA GALACTOSIDASE; BETA LACTOGLOBULIN; BIOLOGICAL MARKER; CARBONATE DEHYDRATASE; CASEIN; FIBRINOGEN; MITOCHONDRIAL PROTEIN; MYOGLOBIN; OVALBUMIN; PLASMINOGEN; RIBONUCLEASE A; TRANSFERRIN; UNCLASSIFIED DRUG;

EID: 33750615386     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M600222-MCP200     Document Type: Article
Times cited : (129)

References (44)
  • 1
    • 23044507211 scopus 로고    scopus 로고
    • Quantitative MS for proteomics: Teaching a new dog old tricks
    • MacCoss, M. J., and Matthews, D. E. (2005) Quantitative MS for proteomics: teaching a new dog old tricks. Anal. Chem. 77, 294A-302A
    • (2005) Anal. Chem. , vol.77
    • MacCoss, M.J.1    Matthews, D.E.2
  • 2
    • 33644524918 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics turns quantitative
    • Ong, S. E., and Mann, M. (2005) Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262
    • (2005) Nat. Chem. Biol. , vol.1 , pp. 252-262
    • Ong, S.E.1    Mann, M.2
  • 3
    • 23944490671 scopus 로고    scopus 로고
    • Place of pattern in proteomic biomarker discovery
    • Gillette, M. A., Mani, D. R., and Carr, S. A. (2005) Place of pattern in proteomic biomarker discovery. J. Proteome Res. 4, 1143-1154
    • (2005) J. Proteome Res. , vol.4 , pp. 1143-1154
    • Gillette, M.A.1    Mani, D.R.2    Carr, S.A.3
  • 4
    • 0001644020 scopus 로고    scopus 로고
    • The human plasma proteome: History, character, and diagnostic prospects
    • Anderson, N. L., and Anderson, N. G. (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1, 845-867
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 845-867
    • Anderson, N.L.1    Anderson, N.G.2
  • 8
    • 1242316198 scopus 로고    scopus 로고
    • Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome
    • Shen, Y., Jacobs, J. M., Camp, D. G., II, Fang, R., Moore, R. J., Smith, R. D., Xiao, W., Davis, R. W., and Tompkins, R. G. (2004) Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal. Chem. 76, 1134-1144
    • (2004) Anal. Chem. , vol.76 , pp. 1134-1144
    • Shen, Y.1    Jacobs, J.M.2    Camp II, D.G.3    Fang, R.4    Moore, R.J.5    Smith, R.D.6    Xiao, W.7    Davis, R.W.8    Tompkins, R.G.9
  • 11
    • 1542617944 scopus 로고    scopus 로고
    • Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry
    • Villanueva, J., Philip, J., Entenberg, D., Chaparro, C. A., Tanwar, M. K., Holland, E. C., and Tempst, P. (2004) Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem. 76, 1560-1570
    • (2004) Anal. Chem. , vol.76 , pp. 1560-1570
    • Villanueva, J.1    Philip, J.2    Entenberg, D.3    Chaparro, C.A.4    Tanwar, M.K.5    Holland, E.C.6    Tempst, P.7
  • 12
    • 10744233766 scopus 로고    scopus 로고
    • Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards
    • Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T. A., Hill, L. R., Norton, S., Kumar, P., Anderle, M., and Becker, C. H. (2003) Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75, 4818-4826
    • (2003) Anal. Chem. , vol.75 , pp. 4818-4826
    • Wang, W.1    Zhou, H.2    Lin, H.3    Roy, S.4    Shaler, T.A.5    Hill, L.R.6    Norton, S.7    Kumar, P.8    Anderle, M.9    Becker, C.H.10
  • 13
    • 33646264529 scopus 로고    scopus 로고
    • Advances in proteomics data analysis and display using an accurate mass and time tag approach
    • Zimmer, J. S., Monroe, M. E., Qian, W. J., and Smith, R. D. (2006) Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom. Rev. 25, 450-482
    • (2006) Mass Spectrom. Rev. , vol.25 , pp. 450-482
    • Zimmer, J.S.1    Monroe, M.E.2    Qian, W.J.3    Smith, R.D.4
  • 14
    • 1242283923 scopus 로고    scopus 로고
    • FTICR mass spectrometry for qualitative and quantitative bioanalyses
    • Page, J. S., Masselon, C. D., and Smith, R. D. (2004) FTICR mass spectrometry for qualitative and quantitative bioanalyses. Curr. Opin. Biotechnol. 15, 3-11
    • (2004) Curr. Opin. Biotechnol. , vol.15 , pp. 3-11
    • Page, J.S.1    Masselon, C.D.2    Smith, R.D.3
  • 15
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K., McCormack, A. L., and Yates, J. R., III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates III, J.R.3
  • 16
    • 0346158344 scopus 로고    scopus 로고
    • Deriving statistical models for predicting peptide tandem MS product ion intensities
    • Schutz, F., Kapp, E. A., Simpson, R. J., and Speed, T. P. (2003) Deriving statistical models for predicting peptide tandem MS product ion intensities. Biochem. Soc. Trans. 31, 1479-1483
    • (2003) Biochem. Soc. Trans. , vol.31 , pp. 1479-1483
    • Schutz, F.1    Kapp, E.A.2    Simpson, R.J.3    Speed, T.P.4
  • 17
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
    • (2002) Anal. Chem. , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 18
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658
    • (2003) Anal. Chem. , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 19
    • 33645467062 scopus 로고    scopus 로고
    • Improved classification of mass spectrometry database search results using newer machine learning approaches
    • Ulintz, P. J., Zhu, J., Qin, Z. S., and Andrews, P. C. (2006) Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol. Cell. Proteomics 5, 497-509
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 497-509
    • Ulintz, P.J.1    Zhu, J.2    Qin, Z.S.3    Andrews, P.C.4
  • 20
    • 14744293536 scopus 로고    scopus 로고
    • Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra
    • Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A., and Yates, J. R. (2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1, 39-45
    • (2004) Nat. Methods , vol.1 , pp. 39-45
    • Venable, J.D.1    Dong, M.Q.2    Wohlschlegel, J.3    Dillin, A.4    Yates, J.R.5
  • 21
    • 0141924429 scopus 로고    scopus 로고
    • Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology
    • Washburn, M. P., Ulaszek, R. R., and Yates, J. R., III (2003) Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology. Anal. Chem. 75, 5054-5061
    • (2003) Anal. Chem. , vol.75 , pp. 5054-5061
    • Washburn, M.P.1    Ulaszek, R.R.2    Yates III, J.R.3
  • 22
    • 23944434470 scopus 로고    scopus 로고
    • A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes
    • Tang, H. Y., Ali-Khan, N., Echan, L. A., Levenkova, N., Rux, J. J., and Speicher, D. W. (2005) A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics 5, 3329-3342
    • (2005) Proteomics , vol.5 , pp. 3329-3342
    • Tang, H.Y.1    Ali-Khan, N.2    Echan, L.A.3    Levenkova, N.4    Rux, J.J.5    Speicher, D.W.6
  • 23
    • 17844394177 scopus 로고    scopus 로고
    • Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry
    • Listgarten, J., and Emili, A. (2005) Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 4, 419-434
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 419-434
    • Listgarten, J.1    Emili, A.2
  • 24
    • 33646252011 scopus 로고    scopus 로고
    • Processing and classification of protein mass spectra Mass
    • Hilario, M., Kalousis, A., Pellegrini, C., and Muller, M. (2006) Processing and classification of protein mass spectra. Mass Spectrom. Rev. 25, 409-449
    • (2006) Spectrom. Rev. , vol.25 , pp. 409-449
    • Hilario, M.1    Kalousis, A.2    Pellegrini, C.3    Muller, M.4
  • 25
    • 0037314884 scopus 로고    scopus 로고
    • High mass measurement accuracy determination for proteomics using multivariate regression fitting: Application to electrospray ionization time-of-flight mass spectrometry
    • Strittmatter, E. F., Rodriguez, N., and Smith, R. D. (2003) High mass measurement accuracy determination for proteomics using multivariate regression fitting: application to electrospray ionization time-of-flight mass spectrometry. Anal. Chem. 75, 460-468
    • (2003) Anal. Chem. , vol.75 , pp. 460-468
    • Strittmatter, E.F.1    Rodriguez, N.2    Smith, R.D.3
  • 28
    • 14344250874 scopus 로고    scopus 로고
    • Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry
    • Radulovic, D., Jelveh, S., Ryu, S., Hamilton, T. G., Foss, E., Mao, Y., and Emili, A. (2004) Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 3, 984-997
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 984-997
    • Radulovic, D.1    Jelveh, S.2    Ryu, S.3    Hamilton, T.G.4    Foss, E.5    Mao, Y.6    Emili, A.7
  • 29
    • 32444446805 scopus 로고    scopus 로고
    • XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
    • Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., and Siuzdak, G. (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78, 779-787
    • (2006) Anal. Chem. , vol.78 , pp. 779-787
    • Smith, C.A.1    Want, E.J.2    O'Maille, G.3    Abagyan, R.4    Siuzdak, G.5
  • 32
    • 0034954376 scopus 로고    scopus 로고
    • Aligning gene expression time series with time warping algorithms
    • Aach, J., and Church, G. M. (2001) Aligning gene expression time series with time warping algorithms. Bioinformatics 17, 495-508
    • (2001) Bioinformatics , vol.17 , pp. 495-508
    • Aach, J.1    Church, G.M.2
  • 35
  • 36
    • 33645463331 scopus 로고    scopus 로고
    • MapQuant: Open-source software for large-scale protein quantification
    • Leptos, K. C., Sarracino, D. A., Jaffe, J. D., Krastins, B., and Church, G. M. (2006) MapQuant: open-source software for large-scale protein quantification. Proteomics 6, 1770-1782
    • (2006) Proteomics , vol.6 , pp. 1770-1782
    • Leptos, K.C.1    Sarracino, D.A.2    Jaffe, J.D.3    Krastins, B.4    Church, G.M.5
  • 37
    • 0027453616 scopus 로고
    • Model-based Gaussian and non-Gaussian clustering
    • Banfield, J. D., and Raftery, A. E. (1993) Model-based Gaussian and non-Gaussian clustering. Biometrics 49, 803-821
    • (1993) Biometrics , vol.49 , pp. 803-821
    • Banfield, J.D.1    Raftery, A.E.2
  • 38
    • 0006441254 scopus 로고    scopus 로고
    • MCLUST: Software for model-based cluster and discriminant analysis
    • in Technical Report No. 342, University of Washington, Seattle, WA
    • Fraley, C., and Raftery, A. E. (1998) MCLUST: software for model-based cluster and discriminant analysis, in Technical Report No. 342, University of Washington, Seattle, WA
    • (1998)
    • Fraley, C.1    Raftery, A.E.2
  • 42
    • 0004249246 scopus 로고
    • 3rd Ed. W. H. Freeman and Co., New York
    • Sokal, R. R., and Rohlf, F. J. (1995) Biometry, 3rd Ed., p. 887, W. H. Freeman and Co., New York
    • (1995) Biometry , pp. 887
    • Sokal, R.R.1    Rohlf, F.J.2
  • 44
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289-300
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.