메뉴 건너뛰기




Volumn 18, Issue 4, 2011, Pages 547-557

Shape-based feature matching improves protein identification via LC-MS and tandem MS

Author keywords

algorithms; biology; computational molecular biology; mapping; mass spectroscopy; protein structure

Indexed keywords

PEPTIDE; PROTEIN;

EID: 79957477249     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0155     Document Type: Article
Times cited : (4)

References (31)
  • 1
    • 0035241690 scopus 로고    scopus 로고
    • Mass spectrometry in proteomics
    • DOI 10.1021/cr990076h
    • Aebersold, R., and Goodlett, R. 2001. Mass spectrometry in proteomics. Chem. Rev. 101, 269-295. (Pubitemid 32325797)
    • (2001) Chemical Reviews , vol.101 , Issue.2 , pp. 269-295
    • Aebersold, R.1    Goodlett, D.R.2
  • 2
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • DOI 10.1038/nature01511
    • Aebersold, R., and Mann, M. 2003. Mass spectrometry-based proteomics. Nature 422, 198-207. (Pubitemid 36362757)
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 4
    • 51949110240 scopus 로고    scopus 로고
    • Optimized time alignment algorithm for LC-MS data: Correlation optimized warping using component detection algorithm-selected mass chromatograms
    • Christin, C., Smilde, A., Hoefsloot, H., et al. 2008. Optimized time alignment algorithm for LC-MS data: correlation optimized warping using component detection algorithm-selected mass chromatograms. Anal. Chem. 80, 7012-7021.
    • (2008) Anal. Chem. , vol.80 , pp. 7012-7021
    • Christin, C.1    Smilde, A.2    Hoefsloot, H.3
  • 5
    • 84936916896 scopus 로고
    • Robust locally weighted regression and smoothing scatterplots
    • Cleveland, W. 1979. Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc. 74, 829-836.
    • (1979) J. Am. Stat. Assoc. , vol.74 , pp. 829-836
    • Cleveland, W.1
  • 6
    • 84947318637 scopus 로고
    • Locally weighted regression: An approach to regression analysis by local fitting
    • Cleveland, W., and Devlin, S. 1988. Locally weighted regression: an approach to regression analysis by local fitting. J. Am. Stat. Assoc. 596-610.
    • (1988) J. Am. Stat. Assoc. , pp. 596-610
    • Cleveland, W.1    Devlin, S.2
  • 7
    • 18744411077 scopus 로고    scopus 로고
    • Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform
    • DOI 10.1002/pmic.200401261
    • Coombes, K.R., Tsavachidis, S., Morris, J.S., et al. 2005. Improved peak detection and quantification of mass spec-trometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the un-decimated discrete wavelet transform. Proteomics 16, 4107-4117. (Pubitemid 41626078)
    • (2005) Proteomics , vol.5 , Issue.16 , pp. 4107-4117
    • Coombes, K.R.1    Tsavachidis, S.2    Morris, J.S.3    Baggerly, K.A.4    Hung, M.-C.5    Kuerer, H.M.6
  • 8
    • 3142702204 scopus 로고    scopus 로고
    • Tandem: Matching proteins with tandem mass spectra
    • Craig, R., and Beavis, R.C. 2004. Tandem: matching proteins with tandem mass spectra. Bioinformatics 20, 4666-4667.
    • (2004) Bioinformatics , vol.20 , pp. 4666-4667
    • Craig, R.1    Beavis, R.C.2
  • 11
    • 38049120466 scopus 로고    scopus 로고
    • Alignment of mass spectrometry data by clique finding and optimization
    • Fasulo, D., Emde, A.K., Wang, L., et al. 2006. Alignment of mass spectrometry data by clique finding and optimization. Lect. Notes Comput. Sci. 4532, 119-129.
    • (2006) Lect. Notes Comput. Sci. , vol.4532 , pp. 119-129
    • Fasulo, D.1    Emde, A.K.2    Wang, L.3
  • 13
    • 34547830862 scopus 로고    scopus 로고
    • A geometric approach for the alignment of liquid chromatography-mass spectrometry data
    • Lange, E., Grpl, C., Schulz-Trieglaff, O., et al. 2007. A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics 23, 273-281.
    • (2007) Bioinformatics , vol.23 , pp. 273-281
    • Lange, E.1    Grpl, C.2    Schulz-Trieglaff, O.3
  • 14
    • 33846455417 scopus 로고    scopus 로고
    • A wavelet-based data pre-processing analysis approach in mass spectrometry
    • Li, X., Li, J., and Yao, X. 2006. A wavelet-based data pre-processing analysis approach in mass spectrometry. Comput. Biol. Med. 37, 509-516.
    • (2006) Comput. Biol. Med. , vol.37 , pp. 509-516
    • Li, X.1    Li, J.2    Yao, X.3
  • 15
    • 17844394177 scopus 로고    scopus 로고
    • Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry
    • DOI 10.1074/mcp.R500005-MCP200
    • Listgarten, J., and Emili, A. 2005. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 4, 419-434. (Pubitemid 40590562)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.4 , pp. 419-434
    • Listgarten, J.1    Emili, A.2
  • 16
    • 33846651082 scopus 로고    scopus 로고
    • Difference detection in lc-ms data for protein biomarker discovery
    • Listgarten, J., Neal, R., Roweis, S., et al. 2006. Difference detection in lc-ms data for protein biomarker discovery. Bioinformatics 23, 198-204.
    • (2006) Bioinformatics , vol.23 , pp. 198-204
    • Listgarten, J.1    Neal, R.2    Roweis, S.3
  • 17
    • 0001457509 scopus 로고
    • Some methods for classification and analysis of multivariate observations
    • MacQueen, J. 1967. Some methods for classification and analysis of multivariate observations. Proc. 5th Berkeley Symp. Math. Stat. Probabil. 281-297.
    • (1967) Proc. 5th Berkeley Symp. Math. Stat. Probabil. , pp. 281-297
    • MacQueen, J.1
  • 20
    • 3843059018 scopus 로고    scopus 로고
    • Georegistration of landsat data via robust matching of multi-resolution features
    • Netanyahu, N., Le Moigne, J., and Masek, J. 2004. Georegistration of landsat data via robust matching of multi-resolution features. IEEE Trans. Geosci. Remote Sensing 1586-1600.
    • (2004) IEEE Trans. Geosci. Remote Sensing , pp. 1586-1600
    • Netanyahu, N.1    Le Moigne, J.2    Masek, J.3
  • 21
    • 35748977591 scopus 로고    scopus 로고
    • Improved model-based, platform-independent feature extraction for mass spectrometry
    • DOI 10.1093/bioinformatics/btm385
    • Noy, K., and Fasulo, D. 2007a. Improved model-based, platform-independent feature extraction for mass spectrometry. Bioinformatics 23, 2528-2535. (Pubitemid 350048354)
    • (2007) Bioinformatics , vol.23 , Issue.19 , pp. 2528-2535
    • Noy, K.1    Fasulo, D.2
  • 22
    • 49049100661 scopus 로고    scopus 로고
    • Robust estimation and graph-based meta clustering for LC-MS feature extraction
    • Noy, K., and Fasulo, D. 2007b. Robust estimation and graph-based meta clustering for LC-MS feature extraction. IEEE Int. Conf. Bioinform. Biomed. 30-236.
    • (2007) IEEE Int. Conf. Bioinform. Biomed. , pp. 30-236
    • Noy, K.1    Fasulo, D.2
  • 23
    • 62549154087 scopus 로고    scopus 로고
    • Retention time alignment algorithms for LC/MS data must consider non-linear shifts
    • Podwojski, K., Fritsch, A., Chamrad, D.C., et al. 2009. Retention time alignment algorithms for LC/MS data must consider non-linear shifts. Bioinformatics 25, 758-764.
    • (2009) Bioinformatics , vol.25 , pp. 758-764
    • Podwojski, K.1    Fritsch, A.2    Chamrad, D.C.3
  • 24
    • 33645468005 scopus 로고    scopus 로고
    • Signal maps for mass spectrometry-based comparative proteomics
    • Prakash, A., Mallick, P., Whiteaker, J., et al. 2006. Signal maps for mass spectrometry-based comparative proteomics. Mol. Cell. Proteomics 5, 423-432.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 423-432
    • Prakash, A.1    Mallick, P.2    Whiteaker, J.3
  • 25
    • 33748490271 scopus 로고    scopus 로고
    • Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping
    • DOI 10.1021/ac0605344
    • Prince, J., and Marcotte, E. 2006. Chromatographic alignment of esi-lc-ms proteomics data sets by ordered ojective interpolated warping. Anal. Chem. 78, 6140-6152. (Pubitemid 44360127)
    • (2006) Analytical Chemistry , vol.78 , Issue.17 , pp. 6140-6152
    • Prince, J.T.1    Marcotte, E.M.2
  • 28
    • 51349105893 scopus 로고    scopus 로고
    • Computational quantification of peptides from LC-MS data
    • Schulz-Trieglaff, O., Hussong, R., Grpl, C., et al. 2008. Computational quantification of peptides from LC-MS data. J. Comput. Biol. 15, 685-704.
    • (2008) J. Comput. Biol. , vol.15 , pp. 685-704
    • Schulz-Trieglaff, O.1    Hussong, R.2    Grpl, C.3
  • 29
    • 42949157310 scopus 로고    scopus 로고
    • Two-dimensional method for time aligning liquid chromatography-mass spectrometry data
    • DOI 10.1021/ac702267h
    • Suits, F., Bischoff R., Lepre, J., et al. 2008. Two-dimensional method for time aligning liquid chromatography-mass spectrometry data. Anal. Chem. 80, 3095-3104. (Pubitemid 351620693)
    • (2008) Analytical Chemistry , vol.80 , Issue.9 , pp. 3095-3104
    • Suits, F.1    Lepre, J.2    Du, P.3    Bischoff, R.4    Horvatovich, P.5
  • 31
    • 4444351752 scopus 로고    scopus 로고
    • Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data
    • Tomasi, G., Van den Berg, F., and Andersson, C. 2004. Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data. J. Chemom. 18, 231-241.
    • (2004) J. Chemom. , vol.18 , pp. 231-241
    • Tomasi, G.1    Van Den2    Berg, F.3    Andersson, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.