메뉴 건너뛰기




Volumn 24, Issue 13, 2008, Pages 1503-1509

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; HYDROPHILICITY; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN CONTENT; PROTEIN DATABASE; PROTEOMICS; QUANTITATIVE ANALYSIS; SALMONELLA TYPHIMURIUM; SHEWANELLA ONEIDENSIS; SUPPORT VECTOR MACHINE; VALIDATION PROCESS; YERSINIA PESTIS;

EID: 46349085804     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn218     Document Type: Article
Times cited : (48)

References (41)
  • 1
    • 33748322018 scopus 로고    scopus 로고
    • Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions
    • Adkins,J.N. et al. (2006) Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Mol. Cell. Proteomics., 5, 1450-1461.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 1450-1461
    • Adkins, J.N.1
  • 2
    • 37549023558 scopus 로고    scopus 로고
    • Advancement in protein inference from shotgun proteomics using peptide detectability
    • Alves,P. et al. (2007) Advancement in protein inference from shotgun proteomics using peptide detectability. Pac. Symp. Biocomput. 12, 409-420.
    • (2007) Pac. Symp. Biocomput , vol.12 , pp. 409-420
    • Alves, P.1
  • 3
    • 0042972838 scopus 로고    scopus 로고
    • A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: Support vector machine classification of peptide MS/MS spectra and SEQUEST scores
    • Anderson,D.C. et al. (2003) A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: Support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res., 2, 137-146.
    • (2003) J. Proteome Res , vol.2 , pp. 137-146
    • Anderson, D.C.1
  • 4
    • 33646177915 scopus 로고    scopus 로고
    • Estimating probabilities of peptide database identifications to LC-FTICR-MS observations
    • Anderson,K.K. et al. (2006) Estimating probabilities of peptide database identifications to LC-FTICR-MS observations. Proteome Sci. 4, 1.
    • (2006) Proteome Sci , vol.4 , pp. 1
    • Anderson, K.K.1
  • 7
    • 21244443812 scopus 로고    scopus 로고
    • The use of proteotypic peptide libraries for protein identification
    • Craig,R. et al. (2005) The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Spectrom., 19 1844-1850.
    • (2005) Rapid Commun. Mass Spectrom , vol.19 , pp. 1844-1850
    • Craig, R.1
  • 9
    • 36448962323 scopus 로고    scopus 로고
    • MudPIT: Multidimensional protein identification technology
    • Delahunty,C.M. and Yates,J.R., 3rd (2007) MudPIT: Multidimensional protein identification technology. BioTechniques, 43, 563, 565, 567.
    • (2007) BioTechniques , vol.43
    • Delahunty, C.M.1    Yates 3rd, J.R.2
  • 10
    • 33644876912 scopus 로고    scopus 로고
    • The Peptide Atlas project
    • Desiere,F. et al. (2006) The Peptide Atlas project. Nucleic Acids Res., 34, D655-D658.
    • (2006) Nucleic Acids Res , vol.34
    • Desiere, F.1
  • 11
    • 0021691817 scopus 로고
    • Analysis of membrane and surface protein sequences with the hydrophobic moment plot
    • Eisenberg,D. et al. (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol., 179, 125-142.
    • (1984) J. Mol. Biol , vol.179 , pp. 125-142
    • Eisenberg, D.1
  • 12
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • Grantham,R. (1974) Amino acid difference formula to help explain protein evolution. Science, 185, 862-864.
    • (1974) Science , vol.185 , pp. 862-864
    • Grantham, R.1
  • 13
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon,I. et al. (2002) Gene selection for cancer classification using support vector machines. Mach. Learn., 46, 389-422.
    • (2002) Mach. Learn , vol.46 , pp. 389-422
    • Guyon, I.1
  • 14
    • 33750967325 scopus 로고    scopus 로고
    • Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics
    • Hixson,K.K. et al. (2006) Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics. J Proteome Res., 5, 3008-3017.
    • (2006) J Proteome Res , vol.5 , pp. 3008-3017
    • Hixson, K.K.1
  • 15
    • 0000448982 scopus 로고
    • Prediction of protein antigenic determinants from amino acid sequences
    • Hopp,T.P. and Woods,K.R. (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl Acad. Sci. USA, 78, 3824-3828.
    • (1981) Proc. Natl Acad. Sci. USA , vol.78 , pp. 3824-3828
    • Hopp, T.P.1    Woods, K.R.2
  • 16
    • 20444459841 scopus 로고    scopus 로고
    • Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns
    • Huang,Y. et al. (2005) Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal. Chem., 77, 5800-5813.
    • (2005) Anal. Chem , vol.77 , pp. 5800-5813
    • Huang, Y.1
  • 17
    • 33644875983 scopus 로고    scopus 로고
    • PRIDE: A public repository of protein and peptide identifications for the proteomics community
    • Jones,P. et al. (2006) PRIDE: A public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res., 34, D659-D663.
    • (2006) Nucleic Acids Res , vol.34
    • Jones, P.1
  • 18
    • 33645461851 scopus 로고    scopus 로고
    • PRISM: A data management system for high-throughput proteomics
    • Kiebel,G.R. et al. (2006) PRISM: A data management system for high-throughput proteomics. Proteomics, 6, 1783-1790.
    • (2006) Proteomics , vol.6 , pp. 1783-1790
    • Kiebel, G.R.1
  • 19
    • 21744435622 scopus 로고    scopus 로고
    • Scoring proteomes with proteotypic peptide probes
    • Kuster,B. et al. (2005) Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mot. Cell Biol., 6, 577-583.
    • (2005) Nat. Rev. Mot. Cell Biol , vol.6 , pp. 577-583
    • Kuster, B.1
  • 20
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte,J. and Doolittle,R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.
    • (1982) J. Mol. Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 21
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation ofa spectral library searching method for peptide identification from MS/MS
    • Lam,H. et al. (2007) Development and validation ofa spectral library searching method for peptide identification from MS/MS. Proteomics, 7, 655-667.
    • (2007) Proteomics , vol.7 , pp. 655-667
    • Lam, H.1
  • 22
    • 84872126889 scopus 로고    scopus 로고
    • AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis
    • Lipton,M.S. et al. (2006) AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis. Methods Biochem. Anal., 49, 113-134.
    • (2006) Methods Biochem. Anal , vol.49 , pp. 113-134
    • Lipton, M.S.1
  • 23
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu,P. et al. (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
  • 24
    • 33846133955 scopus 로고    scopus 로고
    • Computational prediction of proteotypic peptides for quantitative proteomics
    • Mallick,P. et al. (2007) Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol., 25, 125-131.
    • (2007) Nat. Biotechnol , vol.25 , pp. 125-131
    • Mallick, P.1
  • 25
    • 34547156610 scopus 로고    scopus 로고
    • A platform for accurate mass and time analyses of mass spectrometry data
    • May,D. et al. (2007) A platform for accurate mass and time analyses of mass spectrometry data. J. Proteome Res., 6, 2685-2694.
    • (2007) J. Proteome Res , vol.6 , pp. 2685-2694
    • May, D.1
  • 26
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii,A.I. et al. (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
  • 27
    • 0036100116 scopus 로고    scopus 로고
    • Learning gene functional classifications from multiple data types
    • Pavlidis,P. et al. (2002) Learning gene functional classifications from multiple data types. J. Comput. Biol., 9, 401-411.
    • (2002) J. Comput. Biol , vol.9 , pp. 401-411
    • Pavlidis, P.1
  • 28
    • 33746448330 scopus 로고    scopus 로고
    • Improved peptide elation time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information
    • Petritis,K. et al. (2006) Improved peptide elation 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
  • 29
    • 0031466516 scopus 로고    scopus 로고
    • Price.W.D. et al. (1997) Is arginine a zwitterion in the gas phase? J. Am. Chem. Soc., 119, 11988-11989.
    • Price.W.D. et al. (1997) Is arginine a zwitterion in the gas phase? J. Am. Chem. Soc., 119, 11988-11989.
  • 30
    • 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
  • 31
    • 27144463192 scopus 로고    scopus 로고
    • On comparing classifiers: Pitfalls to avoid and recommended approach
    • Salzberg,S.L. (1997) On comparing classifiers: Pitfalls to avoid and recommended approach. Data Min. Knowl. Disc., 1, 317-327.
    • (1997) Data Min. Knowl. Disc , vol.1 , pp. 317-327
    • Salzberg, S.L.1
  • 32
    • 0029768104 scopus 로고    scopus 로고
    • Blackbody infrared radiative dissociation of Bradykinin and its analogues: Energetics. dynamics, and evidence for salt-bridge structures in the gas phase
    • Schnier,P.D. et al. (1996) Blackbody infrared radiative dissociation of Bradykinin and its analogues: Energetics. dynamics, and evidence for salt-bridge structures in the gas phase. J. Am. Chem. Soc., 118, 7178-7189.
    • (1996) J. Am. Chem. Soc , vol.118 , pp. 7178-7189
    • Schnier, P.D.1
  • 33
    • 0036406861 scopus 로고    scopus 로고
    • The use of accurate mass tags for high-throughput microbial proteomics
    • Smith,R.D. et al. (2002a) The use of accurate mass tags for high-throughput microbial proteomics. Omics, 6, 61-90.
    • (2002) Omics , vol.6 , pp. 61-90
    • Smith, R.D.1
  • 34
    • 0036253914 scopus 로고    scopus 로고
    • An accurate mass tag strategy for- quantitative, and high-throughput proteome measurements
    • Smith,R.D. et al. (2002b) An accurate mass tag strategy for- quantitative, and high-throughput proteome measurements. Proteomics 2, 513-523.
    • (2002) Proteomics , vol.2 , pp. 513-523
    • Smith, R.D.1
  • 35
    • 33747885134 scopus 로고    scopus 로고
    • A computational approach toward label-free protein quantification using predicted peptide detectability
    • Tang,H. et al. (2006) A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics, 22 e48l-e488.
    • (2006) Bioinformatics , vol.22
    • Tang, H.1
  • 37
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn,M.P. et al. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol., 19, 242-247.
    • (2001) Nat. Biotechnol , vol.19 , pp. 242-247
    • Washburn, M.P.1
  • 38
    • 36349024645 scopus 로고    scopus 로고
    • Current trends in computational inference from mass spectrometry-based proteomics
    • Webb-Robertson,B.J. and Cannon,W.R. (2007) Current trends in computational inference from mass spectrometry-based proteomics. Brief. Bioinform., 8, 304-317.
    • (2007) Brief. Bioinform , vol.8 , pp. 304-317
    • Webb-Robertson, B.J.1    Cannon, W.R.2
  • 39
    • 0029644596 scopus 로고
    • Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
    • Yates,J.R., 3rd et al. (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem., 67, 1426-1436.
    • (1995) Anal. Chem , vol.67 , pp. 1426-1436
    • Yates 3rd, J.R.1
  • 40
    • 0032159387 scopus 로고    scopus 로고
    • Method to compare collision-induced dissociation spectra of peptides: Potential for library searching and subtractive analysis
    • Yates,J.R., 3rd et al. (1998) Method to compare collision-induced dissociation spectra of peptides: Potential for library searching and subtractive analysis. Anal. Chem., 70, 3557-3565.
    • (1998) Anal. Chem , vol.70 , pp. 3557-3565
    • Yates 3rd, J.R.1
  • 41
    • 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.