메뉴 건너뛰기




Volumn 11, Issue 6, 2011, Pages 1075-1085

Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis

Author keywords

Bioinformatics; Sequence searching; Spectral library; Spectral searching

Indexed keywords

PEPTIDE LIBRARY;

EID: 79952285695     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000492     Document Type: Article
Times cited : (66)

References (37)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 4444335470 scopus 로고    scopus 로고
    • The ABC's (and XYZ's) of peptide sequencing
    • Steen, H., Mann, M., The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell. Biol. 2004, 5, 699-711.
    • (2004) Nat. Rev. Mol. Cell. Biol. , vol.5 , pp. 699-711
    • Steen, H.1    Mann, M.2
  • 3
    • 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., 3rd, 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 3rd, J.R.3
  • 4
    • 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., 3rd., 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.L.2    Yates 3rd, J.R.3
  • 5
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence database using mass spectrometry data
    • Perkins, D. N., Pappin, D. J. C., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence database using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 6
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: matching proteins with tandem mass spectra
    • Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 8
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • Tabb, D. L., Fernando, C. G., Chambers, M. C., MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 2007, 6, 654-661.
    • (2007) J. Proteome Res. , vol.6 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 9
    • 0032159387 scopus 로고    scopus 로고
    • Method to compare collision-induced dissociation spectra of peptides: Ppotential for library searching and subtractive analysis
    • Yates, J. R., 3rd., Morgan, S. F., Gatlin, C. L., Griffin, P. R. et al., Method to compare collision-induced dissociation spectra of peptides: Ppotential for library searching and subtractive analysis. Anal. Chem. 1998, 70, 3557-3565.
    • (1998) Anal. Chem. , vol.70 , pp. 3557-3565
    • Yates 3rd, J.R.1    Morgan, S.F.2    Gatlin, C.L.3    Griffin, P.R.4
  • 10
    • 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
  • 11
    • 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. et al., 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
  • 12
    • 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. 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
  • 13
    • 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. et al., 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
  • 14
    • 63049121561 scopus 로고    scopus 로고
    • A simple workflow to increase MS2 identification rate by subsequent spectral library search
    • Ahrne, E., Masselot, A., Binz, P. A., Müller, M. et al., A simple workflow to increase MS2 identification rate by subsequent spectral library search. Proteomics 2009, 9, 1731-1736.
    • (2009) Proteomics , vol.9 , pp. 1731-1736
    • Ahrne, E.1    Masselot, A.2    Binz, P.A.3    Müller, M.4
  • 16
    • 23944492134 scopus 로고    scopus 로고
    • Overview of the HUPO plasma proteome project: Rresults from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
    • Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W. et al., Overview of the HUPO plasma proteome project: Rresults from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005, 5, 3226-3245.
    • (2005) Proteomics , vol.5 , pp. 3226-3245
    • Omenn, G.S.1    States, D.J.2    Adamski, M.3    Blackwell, T.W.4
  • 17
    • 8344284323 scopus 로고    scopus 로고
    • A common open representation of mass spectrometry data and its application to proteomics research
    • Pedrioli, P. G., Eng, J. K., Hubley, R., Vogelzang, M. et al., A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22, 1459-1466.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1459-1466
    • Pedrioli, P.G.1    Eng, J.K.2    Hubley, R.3    Vogelzang, M.4
  • 18
    • 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., Aebersold, R., Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. J. Proteomics Res. 2010, 9, 605-610.
    • (2010) J. Proteomics Res. , vol.9 , pp. 605-610
    • Lam, H.1    Deutsch, E.W.2    Aebersold, R.3
  • 19
    • 77949676526 scopus 로고    scopus 로고
    • A guided tour of the trans-proteomic pipeline
    • Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T. et al., A guided tour of the trans-proteomic pipeline. Proteomics 2010, 10, 1150-1159.
    • (2010) Proteomics , vol.10 , pp. 1150-1159
    • Deutsch, E.W.1    Mendoza, L.2    Shteynberg, D.3    Farrah, T.4
  • 20
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74, 5383-5392.
    • (2002) Anal. Chem. , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 21
    • 33750979860 scopus 로고    scopus 로고
    • General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
    • MacLean, B., Eng, J. K., Beavis, R. C., McIntosh, M., General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 2006, 22, 2830-2832.
    • (2006) Bioinformatics , vol.22 , pp. 2830-2832
    • Maclean, B.1    Eng, J.K.2    Beavis, R.C.3    Mcintosh, M.4
  • 22
    • 38649083116 scopus 로고    scopus 로고
    • Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling
    • Choi, H., Ghosh, D., Nesvizhskii, A. I., Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J. Proteomics Res. 2008, 7, 286-292.
    • (2008) J. Proteomics Res. , vol.7 , pp. 286-292
    • Choi, H.1    Ghosh, D.2    Nesvizhskii, A.I.3
  • 23
    • 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
  • 24
    • 3242660851 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides
    • Zhang, Z., Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 2004, 76, 3908-3922.
    • (2004) Anal. Chem. , vol.76 , pp. 3908-3922
    • Zhang, Z.1
  • 25
    • 26444607864 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges
    • Zhang, Z., Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 2005, 77, 6364-6373.
    • (2005) Anal. Chem. , vol.77 , pp. 6364-6373
    • Zhang, Z.1
  • 26
    • 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. et al., 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. 2006, 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
  • 27
    • 77957221582 scopus 로고    scopus 로고
    • A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
    • Nesvizhskii, A. I., A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 2010, 73, 2092-2123.
    • (2010) J. Proteomics , vol.73 , pp. 2092-2123
    • Nesvizhskii, A.I.1
  • 28
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii, A. I., Vitek, O., Aebersold, R., Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 2007, 4, 787-797.
    • (2007) Nat. Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 29
    • 70349895748 scopus 로고    scopus 로고
    • Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers
    • Sherwood, C. A., Eastham, A., Lee, L. W., Risler, J. et al., Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. J. Proteome Res. 2009, 8, 4243-4251.
    • (2009) J. Proteome Res. , vol.8 , pp. 4243-4251
    • Sherwood, C.A.1    Eastham, A.2    Lee, L.W.3    Risler, J.4
  • 30
    • 33845453748 scopus 로고    scopus 로고
    • Quality assessment of tandem mass spectra based on cumulative intensity normalization
    • Na, S., Paek, E., Quality assessment of tandem mass spectra based on cumulative intensity normalization. J. Proteome Res. 2006, 5, 3241-3248.
    • (2006) J. Proteome Res. , vol.5 , pp. 3241-3248
    • Na, S.1    Paek, E.2
  • 31
    • 35349021975 scopus 로고    scopus 로고
    • Peptide fragment intensity statistical modeling
    • Colinge, J., Peptide fragment intensity statistical modeling. Anal. Chem. 2007, 79, 7286-7290.
    • (2007) Anal. Chem. , vol.79 , pp. 7286-7290
    • Colinge, J.1
  • 32
    • 77954693858 scopus 로고    scopus 로고
    • Computational analysis of unassigned high-quality MS/MS spectra in proteome data sets
    • Ning, K., Fermin, D., Nesvizhskii, A. I., Computational analysis of unassigned high-quality MS/MS spectra in proteome data sets. Proteomics 2010, 10, 2712-2718.
    • (2010) Proteomics , vol.10 , pp. 2712-2718
    • Ning, K.1    Fermin, D.2    Nesvizhskii, A.I.3
  • 33
    • 66149152717 scopus 로고    scopus 로고
    • A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins
    • Yen, C., Meyer-Arendt, K., Eichelberger, B., Sun, S. et al., A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins. Mol. Cell. Proteomics 2008, 8, 857-869.
    • (2008) Mol. Cell. Proteomics , vol.8 , pp. 857-869
    • Yen, C.1    Meyer-Arendt, K.2    Eichelberger, B.3    Sun, S.4
  • 34
    • 58149391408 scopus 로고    scopus 로고
    • A spectral clustering approach to MS/MS identification of post-translational modifications
    • Falkner, J. A., Falkner, J. W., Yocum, A. K., Andrews, P. C., A spectral clustering approach to MS/MS identification of post-translational modifications. J. Proteome Res. 2008, 7, 4614-4622.
    • (2008) J. Proteome Res. , vol.7 , pp. 4614-4622
    • Falkner, J.A.1    Falkner, J.W.2    Yocum, A.K.3    Andrews, P.C.4
  • 35
    • 77954191980 scopus 로고    scopus 로고
    • Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate
    • Ye, D., Fu, Y., Sun, R., Wang, H. et al., Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. Bioinformatics 2010, 26, i399-i406.
    • (2010) Bioinformatics , vol.26
    • Ye, D.1    Fu, Y.2    Sun, R.3    Wang, H.4
  • 36
    • 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. 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
  • 37
    • 70349972789 scopus 로고    scopus 로고
    • MaRiMba: a software application for spectral library-based MRM transition list assembly
    • Sherwood, C. A., Eastham, A., Lee, L. W., Peterson, A. et al., MaRiMba: a software application for spectral library-based MRM transition list assembly. J. Proteome Res. 2009, 8, 4395-4405.
    • (2009) J. Proteome Res. , vol.8 , pp. 4395-4405
    • Sherwood, C.A.1    Eastham, A.2    Lee, L.W.3    Peterson, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.