메뉴 건너뛰기




Volumn 75, Issue 7, 2012, Pages 2269-2274

Isoelectric point optimization using peptide descriptors and support vector machines

Author keywords

Isoelectric point; Peptide descriptors; Support vector machine

Indexed keywords

AMINO ACID; PEPTIDE;

EID: 84862798576     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.01.029     Document Type: Article
Times cited : (36)

References (26)
  • 1
    • 0027521381 scopus 로고
    • The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences
    • Bjellqvist B., Hughes G.J., Pasquali C., Paquet N., Ravier F., Sanchez J.C., et al. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993, 14:1023-1031.
    • (1993) Electrophoresis , vol.14 , pp. 1023-1031
    • Bjellqvist, B.1    Hughes, G.J.2    Pasquali, C.3    Paquet, N.4    Ravier, F.5    Sanchez, J.C.6
  • 2
    • 47549117421 scopus 로고    scopus 로고
    • Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects
    • Cargile B.J., Sevinsky J.R., Essader A.S., Eu J.P., Stephenson J.L. Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects. Electrophoresis 2008, 29:2768-2778.
    • (2008) Electrophoresis , vol.29 , pp. 2768-2778
    • Cargile, B.J.1    Sevinsky, J.R.2    Essader, A.S.3    Eu, J.P.4    Stephenson, J.L.5
  • 5
    • 2342629293 scopus 로고    scopus 로고
    • Determination of the isoelectric point of proteins by capillary isoelectric focusing
    • Righetti P.G. Determination of the isoelectric point of proteins by capillary isoelectric focusing. J Chromatogr A 2004, 1037:491-499.
    • (2004) J Chromatogr A , vol.1037 , pp. 491-499
    • Righetti, P.G.1
  • 6
    • 57649220813 scopus 로고    scopus 로고
    • A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing
    • Gauci S., van Breukelen B., Lemeer S.M., Krijgsveld J., Heck A.J. A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing. Proteomics 2008, 8:4898-4906.
    • (2008) Proteomics , vol.8 , pp. 4898-4906
    • Gauci, S.1    van Breukelen, B.2    Lemeer, S.M.3    Krijgsveld, J.4    Heck, A.J.5
  • 7
    • 29144480261 scopus 로고    scopus 로고
    • Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides
    • Heller M., Ye M., Michel P.E., Morier P., Stalder D., Junger M.A., et al. Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides. J Proteome Res 2005, 4:2273-2282.
    • (2005) J Proteome Res , vol.4 , pp. 2273-2282
    • Heller, M.1    Ye, M.2    Michel, P.E.3    Morier, P.4    Stalder, D.5    Junger, M.A.6
  • 8
    • 80052022909 scopus 로고    scopus 로고
    • In silico analysis of accurate proteomics, complemented by selective isolation of peptides
    • Perez-Riverol Y., Sanchez A., Ramos Y., Schmidt A., Muller M., Betancourt L., et al. In silico analysis of accurate proteomics, complemented by selective isolation of peptides. J Proteomics 2011, 74:2071-2082.
    • (2011) J Proteomics , vol.74 , pp. 2071-2082
    • Perez-Riverol, Y.1    Sanchez, A.2    Ramos, Y.3    Schmidt, A.4    Muller, M.5    Betancourt, L.6
  • 10
  • 11
    • 65549154236 scopus 로고    scopus 로고
    • Predicting liquid chromatographic retention times of peptides from the Drosophila melanogaster proteome by machine learning approaches
    • Tian F., Yang L., Lv F., Zhou P. Predicting liquid chromatographic retention times of peptides from the Drosophila melanogaster proteome by machine learning approaches. Anal Chim Acta 2009, 644:10-16.
    • (2009) Anal Chim Acta , vol.644 , pp. 10-16
    • Tian, F.1    Yang, L.2    Lv, F.3    Zhou, P.4
  • 12
    • 38149108345 scopus 로고    scopus 로고
    • Enhanced analytical power of SDS-PAGE using machine learning algorithms
    • Supek F., Peharec P., Krsnik-Rasol M., Smuc T. Enhanced analytical power of SDS-PAGE using machine learning algorithms. Proteomics 2008, 8:28-31.
    • (2008) Proteomics , vol.8 , pp. 28-31
    • Supek, F.1    Peharec, P.2    Krsnik-Rasol, M.3    Smuc, T.4
  • 13
    • 16344384583 scopus 로고    scopus 로고
    • Effect of training datasets on support vector machine prediction of protein-protein interactions
    • Lo S.L., Cai C.Z., Chen Y.Z., Chung M.C. Effect of training datasets on support vector machine prediction of protein-protein interactions. Proteomics 2005, 5:876-884.
    • (2005) Proteomics , vol.5 , pp. 876-884
    • Lo, S.L.1    Cai, C.Z.2    Chen, Y.Z.3    Chung, M.C.4
  • 14
    • 27144489164 scopus 로고    scopus 로고
    • A tutorial on support vector machines for pattern recognition
    • Burges C.J.C. A tutorial on support vector machines for pattern recognition. Data Min Knowl Discov 1998, 2:121-167.
    • (1998) Data Min Knowl Discov , vol.2 , pp. 121-167
    • Burges, C.J.C.1
  • 15
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: matching proteins with tandem mass spectra
    • Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 16
    • 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., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 2002, 74:5383-5392.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 17
    • 56249113343 scopus 로고    scopus 로고
    • Building predictive models in R using the caret package
    • Kuhn M. Building predictive models in R using the caret package. J Stat Softw 2008, 28:1-26.
    • (2008) J Stat Softw , vol.28 , pp. 1-26
    • Kuhn, M.1
  • 18
  • 19
    • 0014349825 scopus 로고
    • The characterization of amino acid sequences in proteins by statistical methods
    • Zimmerman J.M., Eliezer N., Simha R. The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 1968, 21:170-201.
    • (1968) J Theor Biol , vol.21 , pp. 170-201
    • Zimmerman, J.M.1    Eliezer, N.2    Simha, R.3
  • 20
    • 38649136585 scopus 로고    scopus 로고
    • High-accuracy peptide mass fingerprinting using peak intensity data with machine learning
    • Yang D., Ramkissoon K., Hamlett E., Giddings M.C. High-accuracy peptide mass fingerprinting using peak intensity data with machine learning. J Proteome Res 2008, 7:62-69.
    • (2008) J Proteome Res , vol.7 , pp. 62-69
    • Yang, D.1    Ramkissoon, K.2    Hamlett, E.3    Giddings, M.C.4
  • 21
    • 57649238001 scopus 로고    scopus 로고
    • Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics
    • Timm W., Scherbart A., Bocker S., Kohlbacher O., Nattkemper T.W. Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics. BMC Bioinformatics 2008, 9:443.
    • (2008) BMC Bioinformatics , vol.9 , pp. 443
    • Timm, W.1    Scherbart, A.2    Bocker, S.3    Kohlbacher, O.4    Nattkemper, T.W.5
  • 24
    • 33750631580 scopus 로고    scopus 로고
    • Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis
    • Horth P., Miller C.A., Preckel T., Wenz C. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol Cell Proteomics 2006, 5:1968-1974.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 1968-1974
    • Horth, P.1    Miller, C.A.2    Preckel, T.3    Wenz, C.4
  • 25
    • 1642485152 scopus 로고    scopus 로고
    • Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides
    • Cargile B.J., Talley D.L., Stephenson J.L. Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides. Electrophoresis 2004, 25:936-945.
    • (2004) Electrophoresis , vol.25 , pp. 936-945
    • Cargile, B.J.1    Talley, D.L.2    Stephenson, J.L.3
  • 26
    • 0347758353 scopus 로고    scopus 로고
    • An alternative to tandem mass spectrometry: isoelectric point and accurate mass for the identification of peptides
    • Cargile B.J., Stephenson J.L. An alternative to tandem mass spectrometry: isoelectric point and accurate mass for the identification of peptides. Anal Chem 2004, 76:267-275.
    • (2004) Anal Chem , vol.76 , pp. 267-275
    • Cargile, B.J.1    Stephenson, J.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.