메뉴 건너뛰기




Volumn 10, Issue 7, 2011, Pages

Spectrum-to-spectrum searching using a proteome-wide spectral library

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE LIBRARY; PROTEOME; PEPTIDE FRAGMENT;

EID: 79960196834     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M111.007666     Document Type: Article
Times cited : (49)

References (35)
  • 1
    • 0034501099 scopus 로고    scopus 로고
    • Mobile and localized protons: A framework for understanding peptide dissociation
    • Wysocki, V. H., Tsaprailis, G., Smith, L. L., and Breci, L. A. (2000) Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass. Spectrom. 35, 1399-1406
    • (2000) J. Mass. Spectrom. , vol.35 , pp. 1399-1406
    • Wysocki, V.H.1    Tsaprailis, G.2    Smith, L.L.3    Breci, L.A.4
  • 3
    • 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
  • 4
    • 26444607864 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges
    • Zhang, Z. (2005) Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 77, 6364-6373
    • (2005) Anal. Chem. , vol.77 , pp. 6364-6373
    • Zhang, Z.1
  • 5
    • 33747626954 scopus 로고    scopus 로고
    • Analysis of Peptide MS/MS Spectra from Large-Scale Proteomics Experiments Using Spectrum Libraries
    • Frewen, B. E., Merrihew, G. E., Wu, C. C., Noble, W. S., and MacCoss, M. J. (2006) Analysis of Peptide MS/MS Spectra from Large-Scale Proteomics Experiments Using Spectrum Libraries. Anal. Chem. 78, 5678-5684
    • (2006) Anal. Chem. , vol.78 , pp. 5678-5684
    • Frewen, B.E.1    Merrihew, G.E.2    Wu, C.C.3    Noble, W.S.4    MacCoss, M.J.5
  • 6
    • 53249098366 scopus 로고    scopus 로고
    • Building consensus spectral libraries for peptide identification in proteomics
    • Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., Stein, S. E., and Aebersold, R. (2008) Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods. 5, 873-875
    • (2008) Nat. Methods. , vol.5 , pp. 873-875
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    Stein, S.E.5    Aebersold, R.6
  • 7
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • DOI 10.1002/pmic.200600625
    • Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., King, N., Stein, S. E., and Aebersold, R. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7, 655-667 (Pubitemid 46453760)
    • (2007) Proteomics , vol.7 , Issue.5 , pp. 655-667
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    King, N.5    Stein, S.E.6    Aebersold, R.7
  • 8
    • 0000881748 scopus 로고
    • Optimization and testing of mass spectral library search algorithms for compound identification
    • Stein, S. E., and Scott, D. R. (1994) Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass. Spectrom. 5, 859-866
    • (1994) J. Am. Soc. Mass. Spectrom. , vol.5 , pp. 859-866
    • Stein, S.E.1    Scott, D.R.2
  • 9
    • 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., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (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
  • 11
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • Tabb, D. L., Fernando, C. G., and Chambers, M. C. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome. Res. 6, 654-661
    • (2007) J. Proteome. Res. , vol.6 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 15
    • 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, 1466-1467
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 16
    • 43349083804 scopus 로고    scopus 로고
    • Using BiblioSpec for creating and searching tandem MS peptide libraries
    • Chapter 13, Unit 13 17
    • Frewen, B., and MacCoss, M. J. (2007) Using BiblioSpec for creating and searching tandem MS peptide libraries. Curr. Protoc. Bioinformatics. Chapter 13, Unit 13 17
    • (2007) Curr. Protoc. Bioinformatics
    • Frewen, B.1    MacCoss, M.J.2
  • 17
    • 3042818018 scopus 로고    scopus 로고
    • The international protein index: An integrated database for proteomics experiments
    • DOI 10.1002/pmic.200300721
    • Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., and Apweiler, R. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4, 1985-1988 (Pubitemid 38880363)
    • (2004) Proteomics , vol.4 , Issue.7 , pp. 1985-1988
    • Kersey, P.J.1    Duarte, J.2    Williams, A.3    Karavidopoulou, Y.4    Birney, E.5    Apweiler, R.6
  • 18
    • 33144462895 scopus 로고    scopus 로고
    • Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: Protease cleavage and SCX elution rules from data mining of MS/MS spectra
    • Yen, C. Y., Russell, S., Mendoza, A. M., Meyer-Arendt, K., Sun, S., Cios, K. J., Ahn, N. G., and Resing, K. A. (2006) Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS spectra. Anal. Chem. 78, 1071-1084
    • (2006) Anal. Chem. , vol.78 , pp. 1071-1084
    • Yen, C.Y.1    Russell, S.2    Mendoza, A.M.3    Meyer-Arendt, K.4    Sun, S.5    Cios, K.J.6    Ahn, N.G.7    Resing, K.A.8
  • 19
    • 0043064042 scopus 로고    scopus 로고
    • A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases
    • Sadygov, R. G., and Yates, J. R., 3rd (2003) A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal. Chem. 75, 3792-3798
    • (2003) Anal. Chem. , vol.75 , pp. 3792-3798
    • Sadygov, R.G.1    Yates III, J.R.2
  • 20
    • 67149093415 scopus 로고    scopus 로고
    • A new probabilistic database search algorithm for ETD spectra
    • Sadygov, R. G., Good, D. M., Swaney, D. L., and Coon, J. J. (2009) A new probabilistic database search algorithm for ETD spectra. J. Proteome. Res. 8, 3198-3205
    • (2009) J. Proteome. Res. , vol.8 , pp. 3198-3205
    • Sadygov, R.G.1    Good, D.M.2    Swaney, D.L.3    Coon, J.J.4
  • 21
    • 0036828724 scopus 로고    scopus 로고
    • Probability-based validation of protein identifications using a modified SEQUEST algorithm
    • MacCoss, M. J., Wu, C. C., and Yates, J. R., 3rd (2002) Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 74, 5593-5599
    • (2002) Anal. Chem. , vol.74 , pp. 5593-5599
    • MacCoss, M.J.1    Wu, C.C.2    Yates III, J.R.3
  • 22
    • 84855186447 scopus 로고    scopus 로고
    • Bioinformatic Evaluation of Datasets Derived from the ABRF sPRG Proteomics Standard
    • Poster available at
    • Lane, W. S., Nesvizhskii, A. I., Searle, B., Tabb, D. L., Kowalak, J. A., and Seymour, S. L. (2007) Bioinformatic Evaluation of Datasets Derived from the ABRF sPRG Proteomics Standard. Poster available at http://www.abrf.org/ ResearchGroups/ProteomicsInformaticsResearchGroup/Studies/sPRG-BIC2007poster. pdf. In ABRF 2007 Tampa, FL
    • (2007) ABRF 2007 Tampa, FL
    • Lane, W.S.1    Nesvizhskii, A.I.2    Searle, B.3    Tabb, D.L.4    Kowalak, J.A.5    Seymour, S.L.6
  • 23
    • 73649110293 scopus 로고    scopus 로고
    • Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics
    • Lam, H., Deutsch, E. W., and Aebersold, R. (2010) Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. J. Proteome. Res. 9, 605-610
    • (2010) J. Proteome. Res. , vol.9 , pp. 605-610
    • Lam, H.1    Deutsch, E.W.2    Aebersold, R.3
  • 24
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods. 4, 207-214
    • (2007) Nat. Methods. , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 25
    • 38649083118 scopus 로고    scopus 로고
    • Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    • Käll, L., Storey, J. D., MacCoss, M. J., and Noble, W. S. (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J. Proteome. Res. 7, 29-34
    • (2008) J. Proteome. Res. , vol.7 , pp. 29-34
    • Käll, L.1    Storey, J.D.2    MacCoss, M.J.3    Noble, W.S.4
  • 26
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genome-wide studies
    • Storey, J. D., and Tibshirani, R. (2003) Statistical significance for genome-wide studies. Proc. Natl. Acad. Sci. U.S.A. 100, 9440-9445
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 27
    • 0037953090 scopus 로고    scopus 로고
    • Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility
    • Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., and Yates, J. R., 3rd (2003) Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal. Chem. 75, 2470-2477
    • (2003) Anal. Chem. , vol.75 , pp. 2470-2477
    • Tabb, D.L.1    MacCoss, M.J.2    Wu, C.C.3    Anderson, S.D.4    Yates III, J.R.5
  • 28
    • 33747736637 scopus 로고    scopus 로고
    • Peptide conformation in gas phase probed by collision-induced dissociation and its correlation to conformation in condensed phases
    • Zhang, Z., and Bordas-Nagy, J. (2006) Peptide conformation in gas phase probed by collision-induced dissociation and its correlation to conformation in condensed phases. J. Am. Soc. Mass. Spectrom. 17, 786-794
    • (2006) J. Am. Soc. Mass. Spectrom. , vol.17 , pp. 786-794
    • Zhang, Z.1    Bordas-Nagy, J.2
  • 30
    • 77954693858 scopus 로고    scopus 로고
    • Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets
    • Ning, K., Fermin, D., and Nesvizhskii, A. I. (2010) Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. Proteomics 10, 2712-2718
    • (2010) Proteomics , vol.10 , pp. 2712-2718
    • Ning, K.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 31
    • 38649136282 scopus 로고    scopus 로고
    • Modes of inference for evaluating the confidence of peptide identifications
    • Fitzgibbon, M., Li, Q., and McIntosh, M. (2008) Modes of inference for evaluating the confidence of peptide identifications. J. Proteome. Res. 7, 35-39
    • (2008) J. Proteome. Res. , vol.7 , pp. 35-39
    • Fitzgibbon, M.1    Li, Q.2    McIntosh, M.3
  • 32
    • 38649090064 scopus 로고    scopus 로고
    • False discovery rates and related statistical concepts in mass spectrometry-based proteomics
    • Choi, H., and Nesvizhskii, A. I. (2008) False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J. Proteome. Res. 7, 47-50
    • (2008) J. Proteome. Res. , vol.7 , pp. 47-50
    • Choi, H.1    Nesvizhskii, A.I.2
  • 33
    • 58149465395 scopus 로고    scopus 로고
    • Decoy methods for assessing false positives and false discovery rates in shotgun proteomics
    • Wang, G., Wu, W. W., Zhang, Z., Masilamani, S., and Shen, R. F. (2009) Decoy methods for assessing false positives and false discovery rates in shotgun proteomics. Anal. Chem. 81, 146-159
    • (2009) Anal. Chem. , vol.81 , pp. 146-159
    • Wang, G.1    Wu, W.W.2    Zhang, Z.3    Masilamani, S.4    Shen, R.F.5
  • 34
    • 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, Morgan, S. F., Gatlin, C. L., Griffin, P. R., and Eng, J. K. (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 III, J.R.1    Morgan, S.F.2    Gatlin, C.L.3    Griffin, P.R.4    Eng, J.K.5
  • 35
    • 79952285695 scopus 로고    scopus 로고
    • Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis
    • Zhang, X., Li, Y., Shao, W., and Lam, H. (2011) Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis. Proteomics 11, 1075-1085
    • (2011) Proteomics , vol.11 , pp. 1075-1085
    • Zhang, X.1    Li, Y.2    Shao, W.3    Lam, H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.