메뉴 건너뛰기




Volumn 26, Issue 13, 2010, Pages 1601-1607

Machine learning based prediction for peptide drift times in ion mobility spectrometry

Author keywords

[No Author keywords available]

Indexed keywords

ION; PEPTIDE;

EID: 77954180132     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq245     Document Type: Article
Times cited : (36)

References (47)
  • 2
    • 34250713877 scopus 로고    scopus 로고
    • Ion mobility spectrometry-mass spectrometry performance using electrodynamic ion funnels and elevated drift gas pressures
    • Baker,E.S. et al. (2007) Ion mobility spectrometry-mass spectrometry performance using electrodynamic ion funnels and elevated drift gas pressures. J. Amer. Soc. Mass Spectrom., 18, 1176-1187.
    • (2007) J. Amer. Soc. Mass Spectrom. , vol.18 , pp. 1176-1187
    • Baker, E.S.1
  • 3
    • 76149102921 scopus 로고    scopus 로고
    • An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies
    • Baker,E.S. et al. (2009) An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J. Proteome Res., 9, 997-1006.
    • (2009) J. Proteome Res. , vol.9 , pp. 997-1006
    • Baker, E.S.1
  • 4
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from primary structure
    • Bock,J.R. and Gough,D.A. (2001) Predicting protein-protein interactions from primary structure. Bioinformatics, 17, 455-460.
    • (2001) Bioinformatics , vol.17 , pp. 455-460
    • Bock, J.R.1    Gough, D.A.2
  • 5
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • Bystroff,C. and Baker,D. (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol., 281, 565-577.
    • (1998) J. Mol. Biol. , vol.281 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 6
    • 77954187780 scopus 로고    scopus 로고
    • LIBSVM: a library for support vector machines. Available at (last accessed date May 14, 2010)
    • Chang,C.-C. and Lin,C.-J. (2001) LIBSVM: a library for support vector machines. Available at http://www.csie.ntu.edu.tw/~cjlin/libsvm (last accessed date May 14, 2010).
    • (2001)
    • Chang, C.-C.1    Lin, C.-J.2
  • 7
    • 0346250790 scopus 로고    scopus 로고
    • Practical selection of SVM parameters and noise estimation for SVM regression
    • Cherkassky,V. and Ma,Y. (2004) Practical selection of SVM parameters and noise estimation for SVM regression. Neural Netw., 17, 113-126.
    • (2004) Neural Netw. , vol.17 , pp. 113-126
    • Cherkassky, V.1    Ma, Y.2
  • 8
    • 0000929505 scopus 로고
    • The hydrophobic moment detects periodicity in protein hydrophobicity
    • Eisenberg,D. et al. (1984) The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl Acad. Sci. USA, 81, 140-144.
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , pp. 140-144
    • Eisenberg, D.1
  • 9
    • 67649666679 scopus 로고    scopus 로고
    • SubCellProt: predicting subcellular localization using machine learning approaches
    • Garg,P. et al. (2009) SubCellProt: predicting subcellular localization using machine learning approaches. In Silico Biol., 9, 35-44.
    • (2009) In Silico Biol. , vol.9 , pp. 35-44
    • Garg, P.1
  • 11
    • 34548567232 scopus 로고    scopus 로고
    • POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions
    • Hirose,S. et al. (2007) POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics, 23, 2046-2053.
    • (2007) Bioinformatics , vol.23 , pp. 2046-2053
    • Hirose, S.1
  • 12
    • 0033556190 scopus 로고    scopus 로고
    • ESI/Ion Trap/Ion Mobility/Time-of-Flight mass spectrometry for rapid and sensitive analysis of biomolecular mixtures
    • Henderson,S.C. et al. (1998) ESI/Ion Trap/Ion Mobility/Time-of-Flight mass spectrometry for rapid and sensitive analysis of biomolecular mixtures. Anal. Chem., 71, 291-301.
    • (1998) Anal. Chem. , vol.71 , pp. 291-301
    • Henderson, S.C.1
  • 13
    • 0002161961 scopus 로고
    • Application of ridge analysis to regression problems
    • Hoerl,A.E. (1962) Application of ridge analysis to regression problems. Chem. Eng. Prog., 58, 54-59.
    • (1962) Chem. Eng. Prog. , vol.58 , pp. 54-59
    • Hoerl, A.E.1
  • 14
    • 0020623947 scopus 로고
    • A computer program for predicting protein antigenic determinants
    • Hopp,T.P. and Woods,K.R. (1983) A computer program for predicting protein antigenic determinants. Mol. Immunol., 20, 483-489.
    • (1983) Mol. Immunol. , vol.20 , pp. 483-489
    • Hopp, T.P.1    Woods, K.R.2
  • 15
    • 62149121444 scopus 로고    scopus 로고
    • Decon2LS: an open source software package for automated processing and visualization of high resolution mass spectrometry data
    • Jaitly,N. et al. (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
  • 16
    • 33750743755 scopus 로고    scopus 로고
    • Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline
    • Jaitly,N. et al. (2006) Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Anal. Chem., 78, 7397-7409.
    • (2006) Anal. Chem. , vol.78 , pp. 7397-7409
    • Jaitly, N.1
  • 17
    • 14044266328 scopus 로고    scopus 로고
    • Profile-based string kernels for remote homology detection and motif extraction
    • IEEE Computer Society, Stanford, CA
    • Kuang,R. et al. (2004) Profile-based string kernels for remote homology detection and motif extraction. In Computational Systems Bioinformatics Conference (CSB'04). IEEE Computer Society, Stanford, CA, pp. 152-160.
    • (2004) Computational Systems Bioinformatics Conference (CSB'04) , pp. 152-160
    • Kuang, R.1
  • 18
    • 17444378757 scopus 로고    scopus 로고
    • Simple probabilistic predictions for support vector regression
    • National Taiwan University
    • Lin,C.-J. and Weng,R.C. (2004) Simple probabilistic predictions for support vector regression. Technical Report, Department of Computer Science, National Taiwan University.
    • (2004) Technical Report, Department of Computer Science
    • Lin, C.-J.1    Weng, R.C.2
  • 19
    • 76049109467 scopus 로고    scopus 로고
    • Prediction of ion drift times for a proteome-wide peptide set using partial least squares regression, least-squares support vector machine and Gaussian process
    • Liu,X. et al. (2009) Prediction of ion drift times for a proteome-wide peptide set using partial least squares regression, least-squares support vector machine and Gaussian process. QSAR Comb. Sci., 28, 1386-1393.
    • (2009) QSAR Comb. Sci. , vol.28 , pp. 1386-1393
    • Liu, X.1
  • 22
    • 34548136221 scopus 로고    scopus 로고
    • VIPER: an advanced software package to support highthroughput LC-MS peptide identification
    • Monroe,M.E. et al. (2007) VIPER: an advanced software package to support highthroughput LC-MS peptide identification. Bioinformatics, 23, 2021-2023.
    • (2007) Bioinformatics , vol.23 , pp. 2021-2023
    • Monroe, M.E.1
  • 23
    • 33646871614 scopus 로고    scopus 로고
    • An ensemble of K-local hyperplanes for predicting protein-protein interactions
    • Nanni,L. and Lumini,A. (2006) An ensemble of K-local hyperplanes for predicting protein-protein interactions. Bioinformatics, 22, 1207-1210.
    • (2006) Bioinformatics , vol.22 , pp. 1207-1210
    • Nanni, L.1    Lumini, A.2
  • 24
    • 31044454399 scopus 로고    scopus 로고
    • Sensitivity and specificity of PLS-class modelling for five sensory characteristics of dry-cured ham using visible and near infrared spectroscopy
    • Ortiz,M.C. et al. (2006) Sensitivity and specificity of PLS-class modelling for five sensory characteristics of dry-cured ham using visible and near infrared spectroscopy. Anal. Chim. Acta, 558, 125-131.
    • (2006) Anal. Chim. Acta , vol.558 , pp. 125-131
    • Ortiz, M.C.1
  • 25
    • 6344280371 scopus 로고    scopus 로고
    • Proteomic analyses using an accurate mass and time tag strategy
    • 626-633, 636 passim
    • Pasa-Tolic,L. et al. (2004) Proteomic analyses using an accurate mass and time tag strategy. Biotechniques, 37, 621-624, 626-633, 636 passim.
    • (2004) Biotechniques , vol.37 , pp. 621-624
    • Pasa-Tolic, L.1
  • 26
    • 12444272753 scopus 로고    scopus 로고
    • Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses
    • Medium: X
    • Petritis,K. et al. (2003) Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. Anal. Chem., 75, 1039-1048, Medium: X.
    • (2003) Anal. Chem. , vol.75 , pp. 1039-1048
    • Petritis, K.1
  • 27
    • 33746448330 scopus 로고    scopus 로고
    • Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information
    • Petritis,K. et al. (2006) Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal. Chem., 78, 5026-5039.
    • (2006) Anal. Chem. , vol.78 , pp. 5026-5039
    • Petritis, K.1
  • 28
    • 84952503562 scopus 로고
    • Thirteen ways to look at the correlation coefficient
    • Rodgers,J.L. and Nicewander,W.A. (1988) Thirteen ways to look at the correlation coefficient. Am. Statist., 42, 59-66.
    • (1988) Am. Statist. , vol.42 , pp. 59-66
    • Rodgers, J.L.1    Nicewander, W.A.2
  • 29
    • 0024278757 scopus 로고
    • Hydrophobicity of the peptide C=O...H-N hydrogen-bonded group
    • Roseman,M.A. (1988) Hydrophobicity of the peptide C=O...H-N hydrogen-bonded group. J. Mol. Biol., 201, 621-623.
    • (1988) J. Mol. Biol. , vol.201 , pp. 621-623
    • Roseman, M.A.1
  • 30
    • 3242885293 scopus 로고    scopus 로고
    • The PredictProtein server
    • Rost,B. et al. (2004) The PredictProtein server. Nucleic Acids Res., 32, W321-W326.
    • (2004) Nucleic Acids Res. , vol.32
    • Rost, B.1
  • 31
    • 0036684871 scopus 로고    scopus 로고
    • Analysis of protein mixtures by matrix-assisted laser desorption ionization-ion mobility-orthogonal-time-of-flight mass spectrometry
    • Ruotolo,B.T. et al. (2002) Analysis of protein mixtures by matrix-assisted laser desorption ionization-ion mobility-orthogonal-time-of-flight mass spectrometry. Int. J. Mass Spectrom., 219, 253-267.
    • (2002) Int. J. Mass Spectrom. , vol.219 , pp. 253-267
    • Ruotolo, B.T.1
  • 32
    • 27144463192 scopus 로고    scopus 로고
    • On comparing classifiers: pitfalls to avoid and a recommended approach
    • Salzberg,S. (1997) On comparing classifiers: pitfalls to avoid and a recommended approach. Data Min Knowl. Discov., 1, 317-328.
    • (1997) Data Min Knowl. Discov. , vol.1 , pp. 317-328
    • Salzberg, S.1
  • 33
    • 0035527773 scopus 로고    scopus 로고
    • Prediction of peptide ion mobilities via a priori calculations from intrinsic size parameters of amino acid residues
    • Shvartsburg,A.A. et al. (2001) Prediction of peptide ion mobilities via a priori calculations from intrinsic size parameters of amino acid residues. J. Am. Soc. Mass Spectrom., 12, 885-888.
    • (2001) J. Am. Soc. Mass Spectrom. , vol.12 , pp. 885-888
    • Shvartsburg, A.A.1
  • 34
    • 4043137356 scopus 로고    scopus 로고
    • A tutorial on support vector regression
    • Smola,A.J. and Scholkopf,B. (2004) A tutorial on support vector regression. Stat. Comput., 14, 199-222.
    • (2004) Stat. Comput. , vol.14 , pp. 199-222
    • Smola, A.J.1    Scholkopf, B.2
  • 35
    • 0032638628 scopus 로고    scopus 로고
    • Least squares support vector machine classifiers
    • Suykens,J.A.K. and Vandewalle,J. (1999) Least squares support vector machine classifiers. Neural Proc. Lett., 9, 293-300.
    • (1999) Neural Proc. Lett. , vol.9 , pp. 293-300
    • Suykens, J.A.K.1    Vandewalle, J.2
  • 36
    • 46049118177 scopus 로고    scopus 로고
    • AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices
    • Tantoso,E. and Li,K.-B. (2008) AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices. Amino Acids, 35, 345-353.
    • (2008) Amino Acids , vol.35 , pp. 345-353
    • Tantoso, E.1    Li, K.-B.2
  • 37
    • 33750313595 scopus 로고    scopus 로고
    • Promoter prediction using physico-chemical properties of DNA
    • Lecture Notes in Computer Science, Springer, Berlin, New York
    • Uren,P. et al. (2006) Promoter prediction using physico-chemical properties of DNA. In Computational Life Sciences II. Vol. 4216 of Lecture Notes in Bioinformatics, Lecture Notes in Computer Science, Springer, Berlin, New York, pp. 21-31.
    • (2006) Computational Life Sciences II. Vol. 4216 of Lecture Notes in Bioinformatics , pp. 21-31
    • Uren, P.1
  • 38
    • 0032238909 scopus 로고    scopus 로고
    • Gas-phase separations of protease digests
    • Valentine,S.J. et al. (1998) Gas-phase separations of protease digests. J. Amer. Soc. Mass Spectrom., 9, 1213-1216.
    • (1998) J. Amer. Soc. Mass Spectrom. , vol.9 , pp. 1213-1216
    • Valentine, S.J.1
  • 39
    • 0033473749 scopus 로고    scopus 로고
    • A database of 660 peptide ion cross sections: use of intrinsic size parameters for bona fide predictions of cross sections
    • Valentine,S.J. et al. (1999a) A database of 660 peptide ion cross sections: use of intrinsic size parameters for bona fide predictions of cross sections. J. Am. Soc. Mass Spectrom., 10, 1188-1211.
    • (1999) J. Am. Soc. Mass Spectrom. , vol.10 , pp. 1188-1211
    • Valentine, S.J.1
  • 40
    • 16644396658 scopus 로고    scopus 로고
    • Intrinsic amino acid size parameters from a series of 113 lysine-terminated tryptic digest peptide ions
    • Valentine,S.J. et al. (1999b) Intrinsic amino acid size parameters from a series of 113 lysine-terminated tryptic digest peptide ions. J. Phys. Chem. B, 103, 1203-1207.
    • (1999) J. Phys. Chem. B , vol.103 , pp. 1203-1207
    • Valentine, S.J.1
  • 42
    • 67650539034 scopus 로고    scopus 로고
    • Prediction of peptide drift time in ion mobility-mass spectrometry
    • Wang,B. et al. (2009) Prediction of peptide drift time in ion mobility-mass spectrometry. BMC Bioinformatics, 10, A1.
    • (2009) BMC Bioinformatics , vol.10
    • Wang, B.1
  • 43
    • 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.M. et al. (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
  • 44
    • 0035965476 scopus 로고    scopus 로고
    • PLS-regression: a basic tool of chemometrics
    • Wold,S. et al. (2001) PLS-regression: a basic tool of chemometrics. Chemometrics Intell. Lab. Syst., 58, 109-130.
    • (2001) Chemometrics Intell. Lab. Syst. , vol.58 , pp. 109-130
    • Wold, S.1
  • 45
    • 41949092513 scopus 로고    scopus 로고
    • Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties
    • Yang,Y. et al. (2008) Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties. J. Theor. Biol., 252, 145-154.
    • (2008) J. Theor. Biol. , vol.252 , pp. 145-154
    • Yang, Y.1
  • 46
    • 3242660851 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides
    • Zhang,Z. (2004) Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem., 76, 3908-3922.
    • (2004) Anal. Chem. , vol.76 , pp. 3908-3922
    • Zhang, Z.1
  • 47
    • 0014349825 scopus 로고
    • The characterization of amino acid sequences in proteins by statistical methods
    • Zimmerman,J.M. et al. (1968) The characterization of amino acid sequences in proteins by statistical methods. J. Theor. Biol., 21, 170-201.
    • (1968) J. Theor. Biol. , vol.21 , pp. 170-201
    • Zimmerman, J.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.