메뉴 건너뛰기




Volumn 81, Issue , 2013, Pages 173-184

A novel spectral library workflow to enhance protein identifications

Author keywords

Error propagation control; Library searching; Noise control; Sliding dot product

Indexed keywords

PEPTIDE; PEPTIDE FRAGMENT; PROTEIN;

EID: 84877876586     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.01.026     Document Type: Article
Times cited : (12)

References (33)
  • 1
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
    • (2001) Nat Biotechnol , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates, J.R.3
  • 3
    • 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., Yates J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994, 5:976-989.
    • (1994) J Am Soc Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.2    Yates, J.R.3
  • 4
    • 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, 20:3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 5
    • 0032159387 scopus 로고    scopus 로고
    • Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis
    • Yates J.R., Morgan S.F., Gatlin C.L., Griffin P.R., Eng J.K. Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis. Anal Chem 1998, 70:3557-3565.
    • (1998) Anal Chem , vol.70 , pp. 3557-3565
    • Yates, J.R.1    Morgan, S.F.2    Gatlin, C.L.3    Griffin, P.R.4    Eng, J.K.5
  • 6
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii A.I., Keller A., Kolker E., Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003, 75:4646-4658.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 7
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: protein modifications for mass spectrometry
    • Creasy D.M., Cottrell J.S. Unimod: protein modifications for mass spectrometry. Proteomics 2004, 4:1534-1536.
    • (2004) Proteomics , vol.4 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 8
    • 70349157281 scopus 로고    scopus 로고
    • Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures
    • Second T.P., Blethrow J.D., Schwartz J.C., Merrihew G.E., MacCoss M.J., Swaney D.L., et al. Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem 2009, 81:7757-7765.
    • (2009) Anal Chem , vol.81 , pp. 7757-7765
    • Second, T.P.1    Blethrow, J.D.2    Schwartz, J.C.3    Merrihew, G.E.4    MacCoss, M.J.5    Swaney, D.L.6
  • 9
    • 67049134015 scopus 로고    scopus 로고
    • Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms
    • Halligan B.D., Geiger J.F., Vallejos A.K., Greene A.S., Twigger S.N. Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms. J Proteome Res 2009, 8:3148-3153.
    • (2009) J Proteome Res , vol.8 , pp. 3148-3153
    • Halligan, B.D.1    Geiger, J.F.2    Vallejos, A.K.3    Greene, A.S.4    Twigger, S.N.5
  • 10
    • 63349110971 scopus 로고    scopus 로고
    • Identification of N-terminally arginylated proteins and peptides by mass spectrometry
    • Xu T., Wong C.C., Kashina A., Yates J.R. Identification of N-terminally arginylated proteins and peptides by mass spectrometry. Nat Protoc 2009, 4:325-332.
    • (2009) Nat Protoc , vol.4 , pp. 325-332
    • Xu, T.1    Wong, C.C.2    Kashina, A.3    Yates, J.R.4
  • 11
    • 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., Aebersold R. Building consensus spectral libraries for peptide identification in proteomics. Nat Methods 2008, 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
  • 12
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias J.E., Gygi S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4:207-214.
    • (2007) Nat Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 13
    • 20144381803 scopus 로고    scopus 로고
    • Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    • Desiere F., Deutsch E.W., Nesvizhskii A.I., Mallick P., King N.L., Eng J.K., et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol 2005, 6:R9.
    • (2005) Genome Biol , vol.6
    • Desiere, F.1    Deutsch, E.W.2    Nesvizhskii, A.I.3    Mallick, P.4    King, N.L.5    Eng, J.K.6
  • 14
    • 36749082830 scopus 로고    scopus 로고
    • Mammalian proteasome subpopulations with distinct molecular compositions and proteolytic activities
    • Drews O., Wildgruber R., Zong C., Sukop U., Nissum M., Weber G., et al. Mammalian proteasome subpopulations with distinct molecular compositions and proteolytic activities. Mol Cell Proteomics 2007, 6:2021-2031.
    • (2007) Mol Cell Proteomics , vol.6 , pp. 2021-2031
    • Drews, O.1    Wildgruber, R.2    Zong, C.3    Sukop, U.4    Nissum, M.5    Weber, G.6
  • 15
    • 61649083080 scopus 로고    scopus 로고
    • Contrasting proteome biology and functional heterogeneity of the 20S proteasome complexes in mammalian tissues
    • Gomes A.V., Young G.W., Wang Y., Zong C., Eghbali M., Drews O., et al. Contrasting proteome biology and functional heterogeneity of the 20S proteasome complexes in mammalian tissues. Mol Cell Proteomics 2009, 8:302-315.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 302-315
    • Gomes, A.V.1    Young, G.W.2    Wang, Y.3    Zong, C.4    Eghbali, M.5    Drews, O.6
  • 16
    • 33747416363 scopus 로고    scopus 로고
    • Regulation of murine cardiac 20S proteasomes: role of associating partners
    • Zong C., Gomes A.V., Drews O., Li X., Young G.W., Berhane B., et al. Regulation of murine cardiac 20S proteasomes: role of associating partners. Circ Res 2006, 99:372-380.
    • (2006) Circ Res , vol.99 , pp. 372-380
    • Zong, C.1    Gomes, A.V.2    Drews, O.3    Li, X.4    Young, G.W.5    Berhane, B.6
  • 17
    • 33947380146 scopus 로고    scopus 로고
    • Mass spectrometric characterization of the affinity-purified human 26S proteasome complex
    • Wang X., Chen C.F., Baker P.R., Chen P.L., Kaiser P., Huang L. Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. Biochemistry 2007, 46:3553-3565.
    • (2007) Biochemistry , vol.46 , pp. 3553-3565
    • Wang, X.1    Chen, C.F.2    Baker, P.R.3    Chen, P.L.4    Kaiser, P.5    Huang, L.6
  • 20
    • 79955758519 scopus 로고    scopus 로고
    • Proteome dynamics and proteome function of cardiac 19S proteasomes
    • [M110 006122]
    • Wang D., Zong C., Koag M.C., Wang Y., Drews O., Fang C., et al. Proteome dynamics and proteome function of cardiac 19S proteasomes. Mol Cell Proteomics 2011, 10. [M110 006122].
    • (2011) Mol Cell Proteomics , vol.10
    • Wang, D.1    Zong, C.2    Koag, M.C.3    Wang, Y.4    Drews, O.5    Fang, C.6
  • 21
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam H., Deutsch E.W., Eddes J.S., Eng J.K., King N., Stein S.E., et al. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 2007, 7:655-667.
    • (2007) Proteomics , vol.7 , 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
  • 22
    • 48949104656 scopus 로고    scopus 로고
    • MzML: a single, unifying data format for mass spectrometer output
    • Deutsch E. mzML: a single, unifying data format for mass spectrometer output. Proteomics 2008, 8:2776-2777.
    • (2008) Proteomics , vol.8 , pp. 2776-2777
    • Deutsch, E.1
  • 23
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: open source software for rapid proteomics tools development
    • Kessner D., Chambers M., Burke R., Agus D., Mallick P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 24:2534-2536.
    • (2008) Bioinformatics , vol.24 , pp. 2534-2536
    • Kessner, D.1    Chambers, M.2    Burke, R.3    Agus, D.4    Mallick, P.5
  • 24
    • 77951965920 scopus 로고    scopus 로고
    • Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
    • MacLean B., Tomazela D.M., Shulman N., Chambers M., Finney G.L., Frewen B., et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26:966-968.
    • (2010) Bioinformatics , vol.26 , pp. 966-968
    • MacLean, B.1    Tomazela, D.M.2    Shulman, N.3    Chambers, M.4    Finney, G.L.5    Frewen, B.6
  • 26
    • 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., MacCoss M.J. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem 2006, 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
  • 27
    • 33747170146 scopus 로고    scopus 로고
    • Using annotated peptide mass spectrum libraries for protein identification
    • Craig R., Cortens J.C., Fenyo D., Beavis R.C. Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res 2006, 5:1843-1849.
    • (2006) J Proteome Res , vol.5 , pp. 1843-1849
    • Craig, R.1    Cortens, J.C.2    Fenyo, D.3    Beavis, R.C.4
  • 28
    • 33745576884 scopus 로고    scopus 로고
    • Recent developments in ion-trap mass spectrometry and related technologies
    • Brancia F.L. Recent developments in ion-trap mass spectrometry and related technologies. Expert Rev Proteomics 2006, 3:143-151.
    • (2006) Expert Rev Proteomics , vol.3 , pp. 143-151
    • Brancia, F.L.1
  • 29
    • 57249091714 scopus 로고    scopus 로고
    • Orbitrap mass spectrometry: instrumentation, ion motion and applications
    • Perry R.H., Cooks R.G., Noll R.J. Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom Rev 2008, 27:661-699.
    • (2008) Mass Spectrom Rev , vol.27 , pp. 661-699
    • Perry, R.H.1    Cooks, R.G.2    Noll, R.J.3
  • 31
    • 79851513271 scopus 로고    scopus 로고
    • Proteomics beyond proteomics: toward clinical applications
    • Plymoth A., Hainaut P. Proteomics beyond proteomics: toward clinical applications. Curr Opin Oncol 2011, 23:77-82.
    • (2011) Curr Opin Oncol , vol.23 , pp. 77-82
    • Plymoth, A.1    Hainaut, P.2
  • 32
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
    • Deutsch E.W., Lam H., Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep 2008, 9:429-434.
    • (2008) EMBO Rep , vol.9 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 33
    • 43349089502 scopus 로고    scopus 로고
    • Validation of tandem mass spectrometry database search results using DTASelect
    • [Chapter 13:Unit 13 4]
    • Cociorva D., Tabb D.L., Yates J.R. Validation of tandem mass spectrometry database search results using DTASelect. Curr Protoc Bioinformatics 2007, [Chapter 13:Unit 13 4].
    • (2007) Curr Protoc Bioinformatics
    • Cociorva, D.1    Tabb, D.L.2    Yates, J.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.