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Volumn 10, Issue 5, 2011, Pages 2306-2317

Large improvements in MS/MS-based peptide identification rates using a hybrid analysis

Author keywords

CO2 fixation; database search; false discovery rate; Peptide identification; spectral library; Synechococcus; tandem mass spectrometry

Indexed keywords

BIOFUEL;

EID: 79955813710     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr101130b     Document Type: Article
Times cited : (19)

References (37)
  • 2
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin, A. C. Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415, 141-147
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1
  • 10
    • 33747885134 scopus 로고    scopus 로고
    • A computational approach toward label-free protein quantification using predicted peptide detectability
    • Tang, H. A computational approach toward label-free protein quantification using predicted peptide detectability Bioinformatics 2006, 22, e481-488
    • (2006) Bioinformatics , vol.22 , pp. 481-488
    • Tang, H.1
  • 11
    • 34447313945 scopus 로고    scopus 로고
    • How do shotgun proteomics algorithms identify proteins?
    • DOI 10.1038/nbt0707-755, PII NBT0707755
    • Marcotte, E. M. How do shotgun proteomics algorithms identify proteins? Nat. Biotechnol. 2007, 25, 755-757 (Pubitemid 47053867)
    • (2007) Nature Biotechnology , vol.25 , Issue.7 , pp. 755-757
    • Marcotte, E.M.1
  • 12
    • 36349024645 scopus 로고    scopus 로고
    • Current trends in computational inference from mass spectrometry-based proteomics
    • DOI 10.1093/bib/bbm023, Special Issue: Current Progress in Bioinformatics: 2007
    • Webb-Robertson, B. J.; Cannon, W. R. Current trends in computational inference from mass spectrometry-based proteomics Brief. Bioinform. 2007, 8 (5) 304-17 (Pubitemid 350142620)
    • (2007) Briefings in Bioinformatics , vol.8 , Issue.5 , pp. 304-317
    • Webb-Robertson, B.-J.M.1    Cannon, W.R.2
  • 13
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, K.; McCormack, A. L.; Yates, J. R., III 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, K.1    McCormack, A.L.2    Yates III, J.R.3
  • 16
    • 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.; Lisacek, F. 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    Lisacek, F.5
  • 17
    • 1842580753 scopus 로고    scopus 로고
    • Improving large-scale proteomics by clustering of mass spectrometry data
    • DOI 10.1002/pmic.200300652
    • Beer, I.; Barnea, E.; Ziv, T.; Admon, A. Improving large-scale proteomics by clustering of mass spectrometry data Proteomics 2004, 4, 950-960 (Pubitemid 38445955)
    • (2004) Proteomics , vol.4 , Issue.4 , pp. 950-960
    • Beer, I.1    Barnea, E.2    Ziv, T.3    Admon, A.4
  • 18
    • 33747170146 scopus 로고    scopus 로고
    • Using annotated peptide mass spectrum libraries for protein identification
    • DOI 10.1021/pr0602085
    • 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 (Pubitemid 44232697)
    • (2006) Journal of Proteome Research , vol.5 , Issue.8 , pp. 1843-1849
    • Craig, R.1    Cortens, J.C.2    Fenyo, D.3    Beavis, R.C.4
  • 19
    • 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.; 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 III, Y.J.1    Morgan, S.F.2    Gatlin, C.L.3    Griffin, P.R.4    Eng, J.K.5
  • 21
    • 34548133443 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for human peptide identification from tandem mass spectrometry
    • Lam, H. Development and validation of a spectral library searching method for human peptide identification from tandem mass spectrometry Mol. Cell. Proteomics 2006, 5, S361-S361
    • (2006) Mol. Cell. Proteomics , vol.5
    • Lam, H.1
  • 22
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • DOI 10.1021/ac025747h
    • Keller, A.; Nesvizhskii, A. I.; Kolker, E.; 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 (Pubitemid 35215372)
    • (2002) Analytical Chemistry , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 25
    • 77950279914 scopus 로고    scopus 로고
    • Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra
    • Cannon, W. R.; Rawlins, M. M. Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra J. Phys. Chem. C 2010, 114, 5360-5366
    • (2010) J. Phys. Chem. C , vol.114 , pp. 5360-5366
    • Cannon, W.R.1    Rawlins, M.M.2
  • 27
    • 77952564899 scopus 로고    scopus 로고
    • Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus
    • Mercer, R. G. Loss of the response regulator CtrA causes pleiotropic effects on gene expression but does not affect growth phase regulation in Rhodobacter capsulatus J. Bacteriol. 2010, 192, 2701-2710
    • (2010) J. Bacteriol. , vol.192 , pp. 2701-2710
    • Mercer, R.G.1
  • 30
    • 35748972060 scopus 로고    scopus 로고
    • Semi-supervised learning for peptide identification from shotgun proteomics datasets
    • DOI 10.1038/nmeth1113, PII NMETH1113
    • Kall, L.; Canterbury, J. D.; Weston, J.; Noble, W. S.; MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets Nat. Methods 2007, 4, 923-925 (Pubitemid 350042380)
    • (2007) Nature Methods , vol.4 , Issue.11 , pp. 923-925
    • Kall, L.1    Canterbury, J.D.2    Weston, J.3    Noble, W.S.4    MacCoss, M.J.5
  • 31
    • 0001070119 scopus 로고
    • Maximum-Likelihood-Estimation of the Parameters of the Generalized Extreme-Value Distribution
    • Hosking, J. R. M. Maximum-Likelihood-Estimation of the Parameters of the Generalized Extreme-Value Distribution Appl. Stat.-J. R. Soc. C 1985, 34, 301-310
    • (1985) Appl. Stat.-J. R. Soc. C , vol.34 , pp. 301-310
    • Hosking, J.R.M.1
  • 32
    • 63549095080 scopus 로고    scopus 로고
    • QVALITY: Non-parametric estimation of q-values and posterior error probabilities
    • Kall, L.; Storey, J. D.; Noble, W. S. QVALITY: non-parametric estimation of q-values and posterior error probabilities Bioinformatics (Oxford, England) 2009, 25, 964-966
    • (2009) Bioinformatics (Oxford, England) , vol.25 , pp. 964-966
    • Kall, L.1    Storey, J.D.2    Noble, W.S.3
  • 34
    • 70349213754 scopus 로고    scopus 로고
    • A bayesian approach to protein inference problem in shotgun proteomics
    • doi: 10.1089/cmb.2009.0018.
    • Li, Y. F. A bayesian approach to protein inference problem in shotgun proteomics. J. Comput. Biol. 16, 1183-1193, doi: 10.1089/cmb.2009.0018 (2009).
    • (2009) J. Comput. Biol , vol.16 , pp. 1183-1193
    • Li, Y.F.1
  • 35
    • 77957339566 scopus 로고    scopus 로고
    • Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data
    • Serang, O.; MacCoss, M. J.; Noble, W. S. Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data J. Proteome Res. 2010, 9, 5346-5357
    • (2010) J. Proteome Res. , vol.9 , pp. 5346-5357
    • Serang, O.1    MacCoss, M.J.2    Noble, W.S.3
  • 36
    • 0037317111 scopus 로고    scopus 로고
    • Intensity-based statistical scorer for tandem mass spectrometry
    • DOI 10.1021/ac0258913
    • Havilio, M.; Haddad, Y.; Smilansky, Z. Intensity-based statistical scorer for tandem mass spectrometry Anal. Chem. 2003, 75, 435-444 (Pubitemid 36176713)
    • (2003) Analytical Chemistry , vol.75 , Issue.3 , pp. 435-444
    • Havilio, M.1    Haddad, Y.2    Smilansky, Z.3


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