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Volumn 13, Issue 5, 2013, Pages 756-765

Extending the coverage of spectral libraries: A neighbor-based approach to predicting intensities of peptide fragmentation spectra

Author keywords

Bioinformatics; High throughput proteomics; Mass spectrometric fragmentation; Spectral library; Tandem mass spectra

Indexed keywords

PROTEOME;

EID: 84874790486     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100670     Document Type: Article
Times cited : (9)

References (42)
  • 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
    • 37249014081 scopus 로고    scopus 로고
    • The biological impact of mass-spectrometry-based proteomics
    • Cravatt, B. F., Simon, G. M., Yates, J. R., The biological impact of mass-spectrometry-based proteomics. Nature 2007, 450, 991-1000.
    • (2007) Nature , vol.450 , pp. 991-1000
    • Cravatt, B.F.1    Simon, G.M.2    Yates, J.R.3
  • 3
    • 3042737683 scopus 로고    scopus 로고
    • Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics
    • Resing, K. A., Meyer-Arendt, K., Mendoza, A. M., Aveline-Wolf, L. D. et al., Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem. 2004, 76, 3556-3568.
    • (2004) Anal. Chem. , vol.76 , pp. 3556-3568
    • Resing, K.A.1    Meyer-Arendt, K.2    Mendoza, A.M.3    Aveline-Wolf, L.D.4
  • 4
    • 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
  • 5
    • 14544300649 scopus 로고    scopus 로고
    • Proteomics strategies for protein identification
    • Resing, K. A., Ahn, N. G., Proteomics strategies for protein identification. FEBS Lett. 2005, 579, 885-889.
    • (2005) FEBS Lett. , vol.579 , pp. 885-889
    • Resing, K.A.1    Ahn, N.G.2
  • 6
    • 33644864034 scopus 로고    scopus 로고
    • Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
    • States, D. J., Omenn, G. S., Blackwell, T. W., Fermin, D. et al., Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 2006, 24, 333-338.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 333-338
    • States, D.J.1    Omenn, G.S.2    Blackwell, T.W.3    Fermin, D.4
  • 7
    • 84873370176 scopus 로고    scopus 로고
    • Computational approaches to protein inference in shotgun proteomics
    • Li, Y. F., Radivojac, P., Computational approaches to protein inference in shotgun proteomics. BMC Bioinformatics, 2012, 13(Suppl 16), S4.
    • (2012) BMC Bioinformatics , vol.13 , Issue.16 SUPPL
    • Li, Y.F.1    Radivojac, P.2
  • 8
    • 37549007898 scopus 로고    scopus 로고
    • Fast and accurate identification of semi-tryptic peptides in shotgun proteomics
    • Alves, P., Arnold, R. J., Clemmer, D. E., Li, Y. et al., Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinformatics 2008, 24, 102-109.
    • (2008) Bioinformatics , vol.24 , pp. 102-109
    • Alves, P.1    Arnold, R.J.2    Clemmer, D.E.3    Li, Y.4
  • 9
    • 33747885134 scopus 로고    scopus 로고
    • A computational approach toward label-free protein quantification using predicted peptide detectability
    • Tang, H., Arnold, R. J., Alves, P., Xun, Z. et al., A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 2006, 22, e481-e488.
    • (2006) Bioinformatics , vol.22
    • Tang, H.1    Arnold, R.J.2    Alves, P.3    Xun, Z.4
  • 10
    • 78649823422 scopus 로고    scopus 로고
    • The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics
    • Li, Y. F., Arnold, R. J., Tang, H., Radivojac, P., The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics. J. Proteome Res. 2010, 9, 6288-6297.
    • (2010) J. Proteome Res. , vol.9 , pp. 6288-6297
    • Li, Y.F.1    Arnold, R.J.2    Tang, H.3    Radivojac, P.4
  • 12
    • 13444304209 scopus 로고    scopus 로고
    • Computational analysis of shotgun proteomics data
    • MacCoss, M. J., Computational analysis of shotgun proteomics data. Curr. Opin. Chem. Biol. 2005, 9, 88-94.
    • (2005) Curr. Opin. Chem. Biol. , vol.9 , pp. 88-94
    • MacCoss, M.J.1
  • 13
    • 71849096141 scopus 로고    scopus 로고
    • How does multiple testing correction work?
    • Noble, W. S., How does multiple testing correction work? Nat. Biotechnol. 2009, 27, 1135-1137.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 1135-1137
    • Noble, W.S.1
  • 14
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: the protein inference problem
    • Nesvizhskii, A. I., Aebersold, R., Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell Proteomics 2005, 4, 1419-1440.
    • (2005) Mol. Cell Proteomics , vol.4 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 15
    • 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
  • 16
    • 0029644596 scopus 로고
    • Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
    • Yates, J. R., Eng, J. K., McCormack, A. L., Schieltz, D., Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 1995, 67, 1426-1436.
    • (1995) Anal. Chem. , vol.67 , pp. 1426-1436
    • Yates, J.R.1    Eng, J.K.2    McCormack, A.L.3    Schieltz, D.4
  • 17
    • 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
  • 18
    • 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
  • 19
    • 0742305695 scopus 로고    scopus 로고
    • Intensity-based protein identification by machine learning from a library of tandem mass spectra
    • Elias, J. E., Gibbons, F. D., King, O. D., Roth, F. P. et al., Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 2004, 22, 214-219.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 214-219
    • Elias, J.E.1    Gibbons, F.D.2    King, O.D.3    Roth, F.P.4
  • 20
    • 79952152636 scopus 로고    scopus 로고
    • On the accuracy and limits of peptide fragmentation spectrum prediction
    • Li, S., Arnold, R. J., Tang, H., Radivojac, P., On the accuracy and limits of peptide fragmentation spectrum prediction. Anal. Chem. 2011, 83, 790-796.
    • (2011) Anal. Chem. , vol.83 , pp. 790-796
    • Li, S.1    Arnold, R.J.2    Tang, H.3    Radivojac, P.4
  • 21
    • 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. et al., 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
  • 22
    • 21244443812 scopus 로고    scopus 로고
    • The use of proteotypic peptide libraries for protein identification
    • Craig, R., Cortens, J. P., Beavis, R. C., The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Spectrom. 2005, 19, 1844-1850.
    • (2005) Rapid Commun. Mass Spectrom. , vol.19 , pp. 1844-1850
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 23
    • 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
  • 24
    • 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
  • 25
    • 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
  • 26
    • 79952123563 scopus 로고    scopus 로고
    • Peptide identification using both spectrum libraries and protein databases
    • Bern, M., Peptide identification using both spectrum libraries and protein databases. Proc. 8th Ann. Int. Conf. Comput. Systems Bioinformatics 2009, 117-126.
    • (2009) Proc. 8th Ann. Int. Conf. Comput. Systems Bioinformatics , pp. 117-126
    • Bern, M.1
  • 27
    • 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., Muller, 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    Muller, M.4
  • 28
    • 79955813710 scopus 로고    scopus 로고
    • Large improvements in MS/MS-based peptide identification rates using a hybrid analysis
    • Cannon, W. R., Rawlins, M. M., Baxter, D. J., Callister, S. J. et al., Large improvements in MS/MS-based peptide identification rates using a hybrid analysis. J. Proteome Res. 2011, 10, 2306-2317.
    • (2011) J. Proteome Res. , vol.10 , pp. 2306-2317
    • Cannon, W.R.1    Rawlins, M.M.2    Baxter, D.J.3    Callister, S.J.4
  • 29
    • 79953676624 scopus 로고    scopus 로고
    • SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry
    • Li, W., Ji, L., Goya, J., Tan, G. et al., SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry. J. Proteome Res. 2011, 10, 1593-1602.
    • (2011) J. Proteome Res. , vol.10 , pp. 1593-1602
    • Li, W.1    Ji, L.2    Goya, J.3    Tan, G.4
  • 30
    • 36348959863 scopus 로고    scopus 로고
    • A machine learning approach to predicting peptide fragmentation spectra
    • Arnold, R. J., Jayasankar, N., Aggarwal, D., Tang, H. et al., A machine learning approach to predicting peptide fragmentation spectra. Pac. Symp. Biocomput. 2006, 11, 219-230.
    • (2006) Pac. Symp. Biocomput. , vol.11 , pp. 219-230
    • Arnold, R.J.1    Jayasankar, N.2    Aggarwal, D.3    Tang, H.4
  • 31
    • 34547732831 scopus 로고    scopus 로고
    • Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS
    • Barton, S. J., Richardson, S., Perkins, D. N., Bellahn, I. et al., Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS. Anal. Chem. 2007, 79, 5601-5607.
    • (2007) Anal. Chem. , vol.79 , pp. 5601-5607
    • Barton, S.J.1    Richardson, S.2    Perkins, D.N.3    Bellahn, I.4
  • 32
    • 46249088907 scopus 로고    scopus 로고
    • Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification
    • Klammer, A. A., Reynolds, S. M., Bilmes, J. A., MacCoss, M. J. et al., Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics 2008, 24, i348-356.
    • (2008) Bioinformatics , vol.24
    • Klammer, A.A.1    Reynolds, S.M.2    Bilmes, J.A.3    MacCoss, M.J.4
  • 33
    • 2442712881 scopus 로고    scopus 로고
    • Impact of ion trap tandem mass spectra variability on the identification of peptides
    • Venable, J. D., Yates, J. R., Impact of ion trap tandem mass spectra variability on the identification of peptides. Anal. Chem. 2004, 76, 2928-2937.
    • (2004) Anal. Chem. , vol.76 , pp. 2928-2937
    • Venable, J.D.1    Yates, J.R.2
  • 35
    • 0003243224 scopus 로고    scopus 로고
    • Probabilistic outputs for support vector machines and comparisons to regularized likelihood methods
    • in: Smola, A. J., Bartlett, P., Scholkopf, B., Schuurmans, D. (Eds.), MIT Press Cambridge USA
    • Platt, J. C., Probabilistic outputs for support vector machines and comparisons to regularized likelihood methods, in: Smola, A. J., Bartlett, P., Scholkopf, B., Schuurmans, D. (Eds.), Advances in Large Margin Classifiers, MIT Press Cambridge USA, 1999, pp. 61-74.
    • (1999) Advances in Large Margin Classifiers , pp. 61-74
    • Platt, J.C.1
  • 36
    • 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. Proteome Res. 2010, 9, 605-610.
    • (2010) J. Proteome Res. , vol.9 , pp. 605-610
    • Lam, H.1    Deutsch, E.W.2    Aebersold, R.3
  • 37
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
    • Tanner, S., Shu, H., Frank, A., Wang, L. C. et al., InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77, 4626-4639.
    • (2005) Anal. Chem. , vol.77 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.C.4
  • 38
    • 21844457685 scopus 로고    scopus 로고
    • Fragmentation pathways of protonated peptides
    • Paizs, B., Suhai, S., Fragmentation pathways of protonated peptides. Mass Spectrom Rev. 2005, 24, 508-548.
    • (2005) Mass Spectrom Rev. , vol.24 , pp. 508-548
    • Paizs, B.1    Suhai, S.2
  • 39
    • 82955197461 scopus 로고    scopus 로고
    • A semi-empirical approach for predicting unobserved peptide MS/MS spectra from spectral libraries
    • Hu Y, Li, Y., Lam, H., A semi-empirical approach for predicting unobserved peptide MS/MS spectra from spectral libraries. Proteomics 2011, 11, 4702-4711.
    • (2011) Proteomics , vol.11 , pp. 4702-4711
    • Hu, Y.1    Li, Y.2    Lam, H.3
  • 40
    • 1642321898 scopus 로고    scopus 로고
    • Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with Ramachandran plots
    • Huang, Y., Triscari, J. M., Pasa-Tolic, L., Anderson, G. A. et al., Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with Ramachandran plots. J. Am. Chem. Soc. 2004, 126, 3034-3035.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 3034-3035
    • Huang, Y.1    Triscari, J.M.2    Pasa-Tolic, L.3    Anderson, G.A.4
  • 41
    • 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., Lam, H., Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis. Proteomics 2011, 11, 1075-1085.
    • (2011) Proteomics , vol.11 , pp. 1075-1085
    • Zhang, X.1    Li, Y.2    Shao, W.3    Lam, H.4
  • 42
    • 79960196834 scopus 로고    scopus 로고
    • Spectrum-to-spectrum searching using a proteome-wide spectral library
    • Yen, C. Y., Houel, S., Ahn, N. G., Old, W. M., Spectrum-to-spectrum searching using a proteome-wide spectral library. Mol. Cell Proteomics 2011, 10, M111 007666.
    • (2011) Mol. Cell Proteomics , vol.10
    • Yen, C.Y.1    Houel, S.2    Ahn, N.G.3    Old, W.M.4


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