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Volumn 14, Issue 2, 2015, Pages 430-440

Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEOME; PEPTIDE LIBRARY;

EID: 84921925151     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M114.044321     Document Type: Article
Times cited : (22)

References (34)
  • 1
    • 84874232489 scopus 로고    scopus 로고
    • The coming age of complete, accurate, and ubiquitous proteomes
    • Mann, M., Kulak, N. A., Nagaraj, N., and Cox, J. (2013) The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell 49, 583-590
    • (2013) Mol. Cell , vol.49 , pp. 583-590
    • Mann, M.1    Kulak, N.A.2    Nagaraj, N.3    Cox, J.4
  • 5
    • 82155179339 scopus 로고    scopus 로고
    • The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells
    • Munoz, J., Low, T. Y., Kok, Y. J., Chin, A., Frese, C. K., Ding, V., Choo, A., and Heck, A. J. (2011) The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol. Sys. Biol. 7, 550
    • (2011) Mol. Sys. Biol , vol.7 , pp. 550
    • Munoz, J.1    Low, T.Y.2    Kok, Y.J.3    Chin, A.4    Frese, C.K.5    Ding, V.6    Choo, A.7    Heck, A.J.8
  • 6
    • 84857938446 scopus 로고    scopus 로고
    • Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins
    • 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 11, M111 014050
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. M110-014050
    • Geiger, T.1    Wehner, A.2    Schaab, C.3    Cox, J.4    Mann, M.5
  • 9
    • 2942598149 scopus 로고    scopus 로고
    • PhosphoSite: A bioinformatics resource dedicated to physiologi-cal protein phosphorylation
    • Hornbeck, P. V., Chabra, I., Kornhauser, J. M., Skrzypek, E., and Zhang, B. (2004) PhosphoSite: a bioinformatics resource dedicated to physiologi-cal protein phosphorylation. Proteomics 4, 1551-1561
    • (2004) Proteomics , vol.4 , pp. 1551-1561
    • Hornbeck, P.V.1    Chabra, I.2    Kornhauser, J.M.3    Skrzypek, E.4    Zhang, B.5
  • 10
    • 0343621535 scopus 로고    scopus 로고
    • AAindex: Amino acid index database
    • Kawashima, S., and Kanehisa, M. (2000) AAindex: amino acid index database. Nucleic Acids Res. 28, 374
    • (2000) Nucleic Acids Res , vol.28 , pp. 374
    • Kawashima, S.1    Kanehisa, M.2
  • 11
    • 84871959637 scopus 로고    scopus 로고
    • Method of the year 2012
    • 2013 Method of the Year 2012. Nature Methods 10, 1-1
    • (2013) Nature Methods , vol.10 , pp. 1-1
  • 12
    • 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 7, S23
    • (2007) BMC Bioinformatics , vol.7 , pp. S23
    • Sanders, W.S.1    Bridges, S.M.2    McCarthy, F.M.3    Nanduri, B.4    Burgess, S.C.5
  • 13
    • 46349085804 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. (2008) A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. Bioinformatics 24, 1503-1509
    • (2008) Bioinformatics , vol.24 , pp. 1503-1509
    • 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
  • 15
    • 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
  • 16
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (em-PAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., and Mann, M. (2005) Exponentially modified protein abundance index (em-PAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 4, 1265-1272
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4    Nagasu, T.5    Rappsilber, J.6    Mann, M.7
  • 17
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu, P., Vogel, C., Wang, R., Yao, X., and Marcotte, E. M. (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25, 117-124
    • (2007) Nat. Biotechnol , vol.25 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.M.5
  • 18
    • 66749190541 scopus 로고    scopus 로고
    • FLEXIQuant: A novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides
    • Singh, S., Springer, M., Steen, J., Kirschner, M. W., and Steen, H. (2009) FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. J. Proteome Res. 8, 2201-2210
    • (2009) J. Proteome Res , vol.8 , pp. 2201-2210
    • Singh, S.1    Springer, M.2    Steen, J.3    Kirschner, M.W.4    Steen, H.5
  • 19
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: Open source software for rapid proteomics tools development
    • Kessner, D., Chambers, M., Burke, R., Agus, D., and Mallick, P. (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 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
  • 20
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p p. B. Range mass accuracies and proteome-wide protein quantification
    • Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372
    • (2008) Nat. Biotechnol , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 27
    • 84872685287 scopus 로고    scopus 로고
    • Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
    • Wisniewski, J. R., Ostasiewicz, P., Dus, K., Zielinska, D. F., Gnad, F., and Mann, M. (2012) Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol. Sys. Biol. 8, 611
    • (2012) Mol. Sys. Biol , vol.8 , pp. 611
    • Wisniewski, J.R.1    Ostasiewicz, P.2    Dus, K.3    Zielinska, D.F.4    Gnad, F.5    Mann, M.6
  • 28
    • 55249096894 scopus 로고    scopus 로고
    • Comprehensive massspectrometry-based proteome quantification of haploid versus diploid yeast
    • de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Frohlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive massspectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254
    • (2008) Nature , vol.455 , pp. 1251-1254
    • De Godoy, L.M.1    Olsen, J.V.2    Cox, J.3    Nielsen, M.L.4    Hubner, N.C.5    Frohlich, F.6    Walther, T.C.7    Mann, M.8
  • 29
    • 0020083498 scopus 로고
    • The meaning and use of the area under a receiver operating characteristic (ROC) curve
    • Hanley, J. A., and McNeil, B. J. (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29-36
    • (1982) Radiology , vol.143 , pp. 29-36
    • Hanley, J.A.1    McNeil, B.J.2
  • 32
    • 0035478854 scopus 로고    scopus 로고
    • In: 45, ed. Machine Learning
    • Breiman, L., (2001) Random Forest, In: 45, ed. Machine Learning, pp. 5-32
    • (2001) Random Forest , pp. 5-32
    • Breiman, L.1
  • 33
    • 84883275474 scopus 로고    scopus 로고
    • Critical assessment of proteome-wide label-free absolute abundance estimation strategies
    • Ahrne, E., Molzahn, L., Glatter, T., and Schmidt, A. (2013) Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics 13, 2567-2578
    • (2013) Proteomics , vol.13 , pp. 2567-2578
    • Ahrne, E.1    Molzahn, L.2    Glatter, T.3    Schmidt, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.