메뉴 건너뛰기




Volumn 10, Issue 11, 2011, Pages

CONSeQuence: Prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

EID: 80053074684     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M110.003384     Document Type: Article
Times cited : (109)

References (43)
  • 4
    • 39749171899 scopus 로고    scopus 로고
    • Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform
    • DOI 10.1021/pr700630x
    • Pan, S., Rush, J., Peskind, E. R., Galasko, D., Chung, K., Quinn, J., Jankovic, J., Leverenz, J. B., Zabetian, C., Pan, C., Wang, Y., Oh, J. H., Gao, J., Zhang, J., Montine, T., and Zhang, J. (2008) Application of Targeted Quantitative Proteomics Analysis in Human Cerebrospinal Fluid Using a Liquid Chromatography Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Tandem Mass Spectrometer (LC MALDI TOF/TOF) Platform. J. Proteome Res. 7, 720-730 (Pubitemid 351294034)
    • (2008) Journal of Proteome Research , vol.7 , Issue.2 , pp. 720-730
    • Pan, S.1    Rush, J.2    Peskind, E.R.3    Galasko, D.4    Chung, K.5    Quinn, J.6    Jankovic, J.7    Leverenz, J.B.8    Zabetian, C.9    Pan, C.10    Wang, Y.11    Jung, H.O.12    Gao, J.13    Zhang, J.14    Montine, T.15    Zhang, J.16
  • 6
    • 23144442824 scopus 로고    scopus 로고
    • Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides
    • DOI 10.1038/nmeth774
    • Beynon, R. J., Doherty, M. K., Pratt, J. M., and Gaskell, S. J. (2005) Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2, 587-589 (Pubitemid 41086849)
    • (2005) Nature Methods , vol.2 , Issue.8 , pp. 587-589
    • Beynon, R.J.1    Doherty, M.K.2    Pratt, J.M.3    Gaskell, S.J.4
  • 8
    • 68449102172 scopus 로고    scopus 로고
    • Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
    • Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E. W., and Aebersold, R. (2009) Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 460, 762-765
    • (2009) Nature , vol.460 , pp. 762-765
    • Malmström, J.1    Beck, M.2    Schmidt, A.3    Lange, V.4    Deutsch, E.W.5    Aebersold, R.6
  • 9
    • 33847179916 scopus 로고    scopus 로고
    • Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes
    • Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J., Gaskell, S. J., and Beynon, R. J. (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. 1, 1029-1043
    • (2006) Nat. Protoc. , vol.1 , pp. 1029-1043
    • Pratt, J.M.1    Simpson, D.M.2    Doherty, M.K.3    Rivers, J.4    Gaskell, S.J.5    Beynon, R.J.6
  • 10
    • 34548427053 scopus 로고    scopus 로고
    • Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT
    • DOI 10.1074/mcp.M600456-MCP200
    • Rivers, J., Simpson, D. M., Robertson, D. H., Gaskell, S. J., and Beynon, R. J. (2007) Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol. Cell. Proteomics 6, 1416-1427 (Pubitemid 47365439)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.8 , pp. 1416-1427
    • Rivers, J.1    Simpson, D.M.2    Robertson, D.H.L.3    Gaskell, S.J.4    Beynon, R.J.5
  • 11
    • 42649091860 scopus 로고    scopus 로고
    • Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics
    • DOI 10.1074/mcp.M700495-MCP200
    • Mirzaei, H., McBee, J. K., Watts, J., and Aebersold, R. (2008) Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol. Cell. Proteomics 7, 813-823 (Pubitemid 351597489)
    • (2008) Molecular and Cellular Proteomics , vol.7 , Issue.4 , pp. 813-823
    • Mirzaei, H.1    McBee, J.K.2    Watts, J.3    Aebersold, R.4
  • 13
    • 20544459800 scopus 로고    scopus 로고
    • Absolute quantification strategies in proteomics based on mass spectrometry
    • Brönstrup, M. (2004) Absolute quantification strategies in proteomics based on mass spectrometry. Expert Rev. Proteomics 1, 503-512
    • (2004) Expert Rev. Proteomics , vol.1 , pp. 503-512
    • Brönstrup, M.1
  • 14
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • DOI 10.1038/nature01511
    • Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207 (Pubitemid 36362757)
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 15
    • 84889414148 scopus 로고    scopus 로고
    • Influence of solvent composition and capillary temperature on the conformations of electrosprayed ions: Unfolding of compact ubiquitin conformers from pseudonative and denatured solutions
    • Li, J., Taraszka, J. A., Counterman, A. E., and Clemmer, D. E. (1999) Influence of solvent composition and capillary temperature on the conformations of electrosprayed ions: unfolding of compact ubiquitin conformers from pseudonative and denatured solutions. Int. J. Mass Spectrom. 185, 37-47
    • (1999) Int. J. Mass Spectrom. , vol.185 , pp. 37-47
    • Li, J.1    Taraszka, J.A.2    Counterman, A.E.3    Clemmer, D.E.4
  • 16
    • 0033214277 scopus 로고    scopus 로고
    • The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins
    • DOI 10.1021/ac990298f
    • Krause, E., Wenschuh, H., and Jungblut, P. R. (1999) The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. Anal. Chem. 71, 4160-4165 (Pubitemid 29466391)
    • (1999) Analytical Chemistry , vol.71 , Issue.19 , pp. 4160-4165
    • Krause, E.1    Wenschuh, H.2    Jungblut, P.R.3
  • 17
    • 0036808751 scopus 로고    scopus 로고
    • Peptide mass fingerprinting peak intensity prediction: Extracting knowledge from spectra
    • DOI 10.1002/1615-9861(200210)2:10<1374::AID-PROT1374>3.0.CO;2-D
    • Gay, S., Binz, P. A., Hochstrasser, D. F., and Appel, R. D. (2002) Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra. Proteomics 2, 1374-1391 (Pubitemid 35340019)
    • (2002) Proteomics , vol.2 , Issue.10 , pp. 1374-1391
    • Gay, S.1    Binz, P.-A.2    Hochstrasser, D.F.3    Appel, R.D.4
  • 18
    • 38349172005 scopus 로고    scopus 로고
    • Prediction of peptides observable by mass spectrometry applied at the experimental set level
    • Sanders, W. S., Bridges, S. M., McCarthy, F. M., Nanduri, B., and Burgess, S. C. (2007) Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinformatics 8, S23
    • (2007) BMC Bioinformatics , vol.8
    • Sanders, W.S.1    Bridges, S.M.2    McCarthy, F.M.3    Nanduri, B.4    Burgess, S.C.5
  • 20
    • 59849093889 scopus 로고    scopus 로고
    • Prediction of high-responding peptides for targeted protein assays by mass spectrometry
    • Fusaro, V. A., Mani, D. R., Mesirov, J. P., and Carr, S. A. (2009) Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat. Biotechnol. 27, 190-198
    • (2009) Nat. Biotechnol. , vol.27 , pp. 190-198
    • Fusaro, V.A.1    Mani, D.R.2    Mesirov, J.P.3    Carr, S.A.4
  • 21
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
    • DOI 10.1038/embor.2008.56, PII EMBOR200856
    • Deutsch, E. W., Lam, H., and Aebersold, R. (2008) PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9, 429-434 (Pubitemid 351627279)
    • (2008) EMBO Reports , vol.9 , Issue.5 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 22
    • 33846632267 scopus 로고    scopus 로고
    • Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics
    • DOI 10.1021/pr060507u
    • Siepen, J. A., Keevil, E. J., Knight, D., and Hubbard, S. J. (2007) Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics. J. Proteome Res. 6, 399-408 (Pubitemid 46173693)
    • (2007) Journal of Proteome Research , vol.6 , Issue.1 , pp. 399-408
    • Siepen, J.A.1    Keevil, E.-J.2    Knight, D.3    Hubbard, S.J.4
  • 23
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • DOI 10.1021/ac025747h
    • 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 (Pubitemid 35215372)
    • (2002) Analytical Chemistry , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 25
    • 0028289435 scopus 로고
    • Determination of free energies of N-capping in alpha-helices by modification of the Lifson-Roig helix-coil theory to include N- and C-capping
    • Doig, A. J., Chakrabartty, A., Klingler, T. M., and Baldwin, R. L. (1994) Determination of free energies of N-capping in alpha-helices by modification of the Lifson-Roig helix-coil therapy to include N- and C-capping. Biochemistry 33, 3396-3403 (Pubitemid 24112654)
    • (1994) Biochemistry , vol.33 , Issue.11 , pp. 3396-3403
    • Doig, A.J.1    Chakrabartty, A.2    Klingler, T.M.3    Baldwin, R.L.4
  • 26
    • 34249753618 scopus 로고
    • SUPPORT-VECTOR NETWORKS
    • Cortes, C., and Vapnik, V. (1995) SUPPORT-VECTOR NETWORKS. Machine Learning 20, 273-297
    • (1995) Machine Learning , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 28
    • 0001938951 scopus 로고    scopus 로고
    • Transductive inference for text classification using Support Vector Machines
    • Bratko, I., and Dzeroski, S., eds. Morgan Kaufmann Pub Inc, San Francisco
    • Joachims, T. (1999) Transductive inference for text classification using Support Vector Machines. In: Bratko, I., and Dzeroski, S., eds. Machine Learning, Proceedings, pp. 200-209, Morgan Kaufmann Pub Inc, San Francisco
    • (1999) Machine Learning, Proceedings , pp. 200-209
    • Joachims, T.1
  • 29
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. (2001) Random forests. Machine Learning 45, 5-32
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 34
    • 0000169232 scopus 로고
    • An algorithm for least-squares estimation of nonlinear parameters
    • Marquardt, D. W. (1963) An algorithm for least-squares estimation of nonlinear parameters. J. Soc. Industr. Appl. Math. 11, 431-441
    • (1963) J. Soc. Industr. Appl. Math. , vol.11 , pp. 431-441
    • Marquardt, D.W.1
  • 36
    • 33747885134 scopus 로고    scopus 로고
    • A computational approach toward label-free protein quantification using predicted peptide detectability
    • DOI 10.1093/bioinformatics/btl237
    • Tang, H., Arnold, R. J., Alves, P., Xun, Z., Clemmer, D. E., Novotny, M. V., Reilly, J. P., and Radivojac, P. (2006) A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 22, e481-488 (Pubitemid 44288319)
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Tang, H.1    Arnold, R.J.2    Alves, P.3    Xun, Z.4    Clemmer, D.E.5    Novotny, M.V.6    Reilly, J.P.7    Radivojac, P.8
  • 37
    • 77954210153 scopus 로고    scopus 로고
    • A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
    • Webb-Robertson, B. J., Cannon, W. R., Oehmen, C. S., Shah, A. R., Gurumoorthi, V., Lipton, M. S., and Waters, K. M. (2010) A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics 26, 1677-1683
    • (2010) Bioinformatics , vol.26 , pp. 1677-1683
    • Webb-Robertson, B.J.1    Cannon, W.R.2    Oehmen, C.S.3    Shah, A.R.4    Gurumoorthi, V.5    Lipton, M.S.6    Waters, K.M.7
  • 40
    • 0031930082 scopus 로고    scopus 로고
    • The ease of peptide detection by matrix-assisted laser desorption/ionization mass spectrometry: The effect of secondary structure on signal intensity
    • DOI 10.1002/(SICI)1097-0231(19980214)12:3<115::AID-RCM124>3.0.CO;2- 5
    • Wenschuh, H., Halada, P., Lamer, S., Jungblut, P., and Krause, E. (1998) The ease of peptide detection by matrix-assisted laser desorption/ionization mass spectrometry: the effect of secondary structure on signal intensity. Rapid Commun. Mass Spectrom. 12, 115-119 (Pubitemid 28073308)
    • (1998) Rapid Communications in Mass Spectrometry , vol.12 , Issue.3 , pp. 115-119
    • Wenschuh, H.1    Halada, P.2    Lamer, S.3    Jungblut, P.4    Krause, E.5
  • 41
    • 69549121810 scopus 로고    scopus 로고
    • The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions
    • Tao, L., Dahl, D. B., Pérez, L. M., and Russell, D. H. (2009) The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions. J. Am. Soc. Mass Spectrom. 20, 1593-1602
    • (2009) J. Am. Soc. Mass Spectrom. , vol.20 , pp. 1593-1602
    • Tao, L.1    Dahl, D.B.2    Pérez, L.M.3    Russell, D.H.4
  • 42
    • 0026058806 scopus 로고
    • Physical reasons for secondary structure stability: Alpha-helices in short peptides
    • Finkelstein, A. V., Badretdinov, A. Y., and Ptitsyn, O. B. (1991) Physical reasons for secondary structure stability: alpha-helices in short peptides. Proteins 10, 287-299
    • (1991) Proteins , vol.10 , pp. 287-299
    • Finkelstein, A.V.1    Badretdinov, A.Y.2    Ptitsyn, O.B.3
  • 43
    • 0023192524 scopus 로고
    • Peptide quantitative structure-activity relationships, a multivariate approach
    • Hellberg, S., Sjöstrom, M., Skagerberg, B., and Wold, S. (1987) Peptide quantitative structure-activity relationships, a multivariate approach. J. Med. Chem. 30, 1126-1135 (Pubitemid 17117970)
    • (1987) Journal of Medicinal Chemistry , vol.30 , Issue.7 , pp. 1126-1135
    • Hellberg, S.1    Sjostrom, M.2    Skagerberg, B.3    Wold, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.