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Volumn 10, Issue 4, 2011, Pages 2095-2103

SVM model for quality assessment of medium resolution mass spectra from 18O-water labeling experiments

Author keywords

isotope distribution; mass accuracy; signal to noise ratio; stable isotope labeling; Support vector machines

Indexed keywords

BOVINE SERUM ALBUMIN; OXYGEN 18;

EID: 79953696551     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr1012174     Document Type: Article
Times cited : (7)

References (48)
  • 1
    • 66749114309 scopus 로고    scopus 로고
    • 2-labeling in quantitative proteomic strategies: A status report
    • 2-labeling in quantitative proteomic strategies: a status report J. Proteome Res. 2009, 8, 2140-43
    • (2009) J. Proteome Res. , vol.8 , pp. 2140-43
    • Fenselau, C.1    Yao, X.2
  • 2
    • 0035384687 scopus 로고    scopus 로고
    • 18O labeling for comparative proteomics: Model studies with two serotypes of adenovirus
    • DOI 10.1021/ac001404c
    • 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus Anal. Chem. 2001, 73, 2836-42 (Pubitemid 32868136)
    • (2001) Analytical Chemistry , vol.73 , Issue.13 , pp. 2836-2842
    • Yao, X.1    Freas, A.2    Ramirez, J.3    Demirev, P.A.4    Fenselau, C.5
  • 3
    • 0030068923 scopus 로고    scopus 로고
    • 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry
    • 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry Electrophoresis 1996, 17, 945-53
    • (1996) Electrophoresis , vol.17 , pp. 945-53
    • Schnolzer, M.1    Jedrzejewski, P.2    Lehmann, W.D.3
  • 5
    • 33846105280 scopus 로고    scopus 로고
    • 18O-labeling strategies for quantitative proteomics
    • DOI 10.1002/mas.20116
    • 18O-labeling strategies for quantitative proteomics Mass Spectrom. Rev. 2007, 26, 121-36 (Pubitemid 46061256)
    • (2007) Mass Spectrometry Reviews , vol.26 , Issue.1 , pp. 121-136
    • Miyagi, M.1    Rao, K.C.S.2
  • 13
  • 14
    • 77952063827 scopus 로고    scopus 로고
    • A regularized method for peptide quantification
    • Yang, C.; Yang, C.; Yu, W. A regularized method for peptide quantification J. Proteome Res. 2010, 9, 2705-12
    • (2010) J. Proteome Res. , vol.9 , pp. 2705-12
    • Yang, C.1    Yang, C.2    Yu, W.3
  • 15
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics. 2002, 1, 376-86
    • (2002) Mol. Cell. Proteomics. , vol.1 , pp. 376-86
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 16
    • 58149401890 scopus 로고    scopus 로고
    • The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses
    • Bakalarski, C. E.; Elias, J. E.; Villen, J.; Haas, W.; Gerber, S. A.; Everley, P. A.; Gygi, S. P. The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses J. Proteome Res. 2008, 7, 4756-65
    • (2008) J. Proteome Res. , vol.7 , pp. 4756-65
    • Bakalarski, C.E.1    Elias, J.E.2    Villen, J.3    Haas, W.4    Gerber, S.A.5    Everley, P.A.6    Gygi, S.P.7
  • 17
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • DOI 10.1023/A:1010933404324
    • Breiman, L. Random forests Machine Learning 2001, 45, 5-32 (Pubitemid 32933532)
    • (2001) Machine Learning , vol.45 , Issue.1 , pp. 5-32
    • Breiman, L.1
  • 18
    • 67049132385 scopus 로고    scopus 로고
    • Software platform for rapidly creating computational tools for mass spectrometry-based proteomics
    • May, D.; Law, W.; Fitzgibbon, M.; Fang, Q.; McIntosh, M. Software platform for rapidly creating computational tools for mass spectrometry-based proteomics J. Proteome Res. 2009, 8, 3212-17
    • (2009) J. Proteome Res. , vol.8 , pp. 3212-17
    • May, D.1    Law, W.2    Fitzgibbon, M.3    Fang, Q.4    McIntosh, M.5
  • 20
    • 34547727671 scopus 로고    scopus 로고
    • High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry
    • DOI 10.1021/ac0700833
    • Hoopmann, M. R.; Finney, G. L.; MacCoss, M. J. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry Anal. Chem. 2007, 79, 5620-32 (Pubitemid 47229808)
    • (2007) Analytical Chemistry , vol.79 , Issue.15 , pp. 5620-5632
    • Hoopmann, M.R.1    Finney, G.L.2    MacCoss, M.J.3
  • 21
    • 33344456468 scopus 로고    scopus 로고
    • Algorithms for automatic interpretation of high resolution mass spectra
    • DOI 10.1016/j.jasms.2005.11.024, PII S1044030505009840
    • Kaur, P.; OConnor, P. B. Algorithms for automatic interpretation of high resolution mass spectra J. Am. Soc. Mass Spectrom. 2006, 17, 459-68 (Pubitemid 43290204)
    • (2006) Journal of the American Society for Mass Spectrometry , vol.17 , Issue.3 , pp. 459-468
    • Kaur, P.1    O'Connor, P.B.2
  • 22
    • 33646730580 scopus 로고    scopus 로고
    • Automatic deconvolution of isotope-resolved mass spectra using variable selection and quantized peptide mass distribution
    • Du, P.; Angeletti, R. H. Automatic deconvolution of isotope-resolved mass spectra using variable selection and quantized peptide mass distribution Anal. Chem. 2006, 78, 3385-92
    • (2006) Anal. Chem. , vol.78 , pp. 3385-92
    • Du, P.1    Angeletti, R.H.2
  • 23
    • 0032594959 scopus 로고    scopus 로고
    • An overview of statistical learning theory
    • Vapnik, V. N. An overview of statistical learning theory IEEE Trans. Neural Netw. 1999, 10, 988-99
    • (1999) IEEE Trans. Neural Netw. , vol.10 , pp. 988-99
    • Vapnik, V.N.1
  • 24
    • 65549119729 scopus 로고    scopus 로고
    • Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments
    • Schulz-Trieglaff, O.; Machtejevas, E.; Reinert, K.; Schluter, H.; Thiemann, J.; Unger, K. Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments BioData Min. 2009, 2, 4
    • (2009) BioData Min. , vol.2 , pp. 4
    • Schulz-Trieglaff, O.1    MacHtejevas, E.2    Reinert, K.3    Schluter, H.4    Thiemann, J.5    Unger, K.6
  • 26
    • 51649130184 scopus 로고    scopus 로고
    • 18O labeling over a coffee break: A rapid strategy for quantitative proteomics
    • 18O labeling over a coffee break: a rapid strategy for quantitative proteomics J. Proteome Res. 2008, 7, 3042-48
    • (2008) J. Proteome Res. , vol.7 , pp. 3042-48
    • Mirza, S.P.1    Greene, A.S.2    Olivier, M.3
  • 27
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20, 3551-67 (Pubitemid 30007252)
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 28
    • 0028575316 scopus 로고
    • Error-tolerant identification of peptides in sequence databases by peptide sequence tags
    • Mann, M.; Wilm, M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags Anal. Chem. 1994, 66, 4390-99 (Pubitemid 124006101)
    • (1994) Analytical Chemistry , vol.66 , Issue.24 , pp. 4390-4399
    • Mann, M.1    Wilm, M.2
  • 29
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K.; McCormack, A. L.; Yates, J. R., III An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5, 976-89
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-89
    • Eng, J.K.1    McCormack, A.L.2    Yates III, J.R.3
  • 30
    • 30044442277 scopus 로고    scopus 로고
    • Central limit theorem as an approximation for intensity-based scoring function
    • DOI 10.1021/ac051206r
    • Sadygov, R.; Wohlschlegel, J.; Park, S. K.; Xu, T.; Yates, J. R., III Central limit theorem as an approximation for intensity-based scoring function Anal. Chem. 2006, 78, 89-95 (Pubitemid 43050142)
    • (2006) Analytical Chemistry , vol.78 , Issue.1 , pp. 89-95
    • Sadygov, R.1    Wohlschlegel, J.2    Park, S.K.3    Xu, T.4    Yates III, J.R.5
  • 31
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • DOI 10.1093/bioinformatics/bth092
    • Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20, 1466-67 (Pubitemid 38931421)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 33
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • DOI 10.1021/ac050102d
    • Tanner, S.; Shu, H.; Frank, A.; Wang, L. C.; Zandi, E.; Mumby, M.; Pevzner, P. A.; Bafna, V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra Anal. Chem. 2005, 77, 4626-39 (Pubitemid 41542287)
    • (2005) Analytical Chemistry , vol.77 , Issue.14 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.-C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 34
    • 0034794886 scopus 로고    scopus 로고
    • Informatics and multiplexing of intact protein identification in bacteria and the archaea
    • DOI 10.1038/nbt1001-952
    • Meng, F.; Cargile, B. J.; Miller, L. M.; Forbes, A. J.; Johnson, J. R.; Kelleher, N. L. Informatics and multiplexing of intact protein identification in bacteria and the archaea Nat. Biotechnol. 2001, 19, 952-57 (Pubitemid 32947574)
    • (2001) Nature Biotechnology , vol.19 , Issue.10 , pp. 952-957
    • Meng, F.1    Cargile, B.J.2    Miller, L.M.3    Forbes, A.J.4    Johnson, J.R.5    Kelleher, N.L.6
  • 35
    • 44949220152 scopus 로고    scopus 로고
    • Comprehensive analysis of the mouse renal cortex using two-dimensional HPLC - Tandem mass spectrometry
    • Zhao, Y.; Denner, L.; Haidacher, S. J.; LeJeune, W. S.; Tilton, R. G. Comprehensive analysis of the mouse renal cortex using two-dimensional HPLC - tandem mass spectrometry Proteome Sci. 2008, 6, 15
    • (2008) Proteome Sci. , vol.6 , pp. 15
    • Zhao, Y.1    Denner, L.2    Haidacher, S.J.3    Lejeune, W.S.4    Tilton, R.G.5
  • 36
    • 0001677717 scopus 로고
    • Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
    • Benjamini, Y.; Hochberg, Y. Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing J. R. Stat. Soc. 1995, 57, 289-300
    • (1995) J. R. Stat. Soc. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 38
    • 0036209134 scopus 로고    scopus 로고
    • Qscore: An algorithm for evaluating SEQUEST database search results
    • DOI 10.1016/S1044-0305(02)00352-5, PII S1044030502003525
    • Moore, R. E.; Young, M. K.; Lee, T. D. Qscore: an algorithm for evaluating SEQUEST database search results J. Am. Soc. Mass Spectrom. 2002, 13, 378-86 (Pubitemid 34280088)
    • (2002) Journal of the American Society for Mass Spectrometry , vol.13 , Issue.4 , pp. 378-386
    • Moore, R.E.1    Young, M.K.2    Lee, T.D.3
  • 39
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • DOI 10.1038/nmeth1019, PII NMETH1019
    • Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4, 207-14 (Pubitemid 46358868)
    • (2007) Nature Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 40
    • 77955445447 scopus 로고    scopus 로고
    • Using power spectrum analysis to evaluate (18)O-water labeling data acquired from low resolution mass spectrometers
    • Sadygov, R. G.; Zhao, Y.; Haidacher, S. J.; Starkey, J. M.; Tilton, R. G.; Denner, L. Using power spectrum analysis to evaluate (18)O-water labeling data acquired from low resolution mass spectrometers J. Proteome Res. 2010, 9, 4306-12
    • (2010) J. Proteome Res. , vol.9 , pp. 4306-12
    • Sadygov, R.G.1    Zhao, Y.2    Haidacher, S.J.3    Starkey, J.M.4    Tilton, R.G.5    Denner, L.6
  • 42
    • 0034582319 scopus 로고    scopus 로고
    • Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules
    • DOI 10.1016/S1044-0305(99)00157-9, PII S1044030599001579
    • Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules J. Am. Soc. Mass Spectrom. 2000, 11, 320-32 (Pubitemid 34516332)
    • (2000) Journal of the American Society for Mass Spectrometry , vol.11 , Issue.4 , pp. 320-332
    • Horn, D.M.1    Zubarev, R.A.2    McLafferty, F.W.3
  • 45
    • 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
    • DOI 10.1021/pr0255654
    • Anderson, D. C.; Li, W.; Payan, D. G.; Noble, W. S. 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. 2003, 2, 137-46 (Pubitemid 37099049)
    • (2003) Journal of Proteome Research , vol.2 , Issue.2 , pp. 137-146
    • Anderson, D.C.1    Li, W.2    Payan, D.G.3    Noble, W.S.4
  • 46
    • 79951480123 scopus 로고    scopus 로고
    • R Development Core Team; R Foundation for Statistical Computing: Vienna, Austria.
    • R Development Core Team R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2010.
    • (2010) R: A Language and Environment for Statistical Computing
  • 48
    • 66749171697 scopus 로고    scopus 로고
    • Statistical design of quantitative mass spectrometry-based proteomic experiments
    • Oberg, A. L.; Vitek, O. Statistical design of quantitative mass spectrometry-based proteomic experiments J. Proteome Res. 2009, 8, 2144-56
    • (2009) J. Proteome Res. , vol.8 , pp. 2144-56
    • Oberg, A.L.1    Vitek, O.2


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