메뉴 건너뛰기




Volumn 13, Issue 5, 2014, Pages 1359-1368

Transferred subgroup false discovery rate for rare post-translational modifications detected by mass spectrometry

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLATION; ALGORITHM; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CARBAMOYLATION; KERNEL METHOD; LIQUID CHROMATOGRAPHY; PRIORITY JOURNAL; PROBABILITY; PROTEIN DATABASE; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; TANDEM MASS SPECTROMETRY; TRANSFERRED SUBGROUP FALSE DISCOVERY RATE; CHEMISTRY; MASS SPECTROMETRY; PROCEDURES; REPRODUCIBILITY; STATISTICS AND NUMERICAL DATA;

EID: 84899714889     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O113.030189     Document Type: Article
Times cited : (72)

References (30)
  • 3
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 4
    • 0037338365 scopus 로고    scopus 로고
    • Proteomic analysis of post-translational modifications
    • Mann, M., and Jensen, O. N. (2003) Proteomic analysis of post-translational modifications. Nat. Biotechnol. 21, 255-261
    • (2003) Nat. Biotechnol. , vol.21 , pp. 255-261
    • Mann, M.1    Jensen, O.N.2
  • 5
    • 35848970747 scopus 로고    scopus 로고
    • Mapping protein post-translational modifications with mass spectrometry
    • Witze, E. S., Old, W. M., Resing, K. A., and Ahn, N. G. (2007) Mapping protein post-translational modifications with mass spectrometry. Nat. Methods 4, 798-806
    • (2007) Nat. Methods , vol.4 , pp. 798-806
    • Witze, E.S.1    Old, W.M.2    Resing, K.A.3    Ahn, N.G.4
  • 6
    • 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., and Yates, J. R., III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass. Spectrom. 5, 976-989
    • (1994) J. Am. Soc. Mass. Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates III, J.R.3
  • 7
    • 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
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 8
    • 4444237022 scopus 로고    scopus 로고
    • Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry
    • Fu, Y., Yang, Q., Sun, R., Li, D., Zeng, R., Ling, C. X., and Gao, W. (2004) Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. Bioinformatics 20, 1948-1954
    • (2004) Bioinformatics , vol.20 , pp. 1948-1954
    • Fu, Y.1    Yang, Q.2    Sun, R.3    Li, D.4    Zeng, R.5    Ling, C.X.6    Gao, W.7
  • 9
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii, A. I., Vitek, O., and Aebersold, R. (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4, 787-797
    • (2007) Nat. Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 10
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Methodol. 57, 289-300
    • (1995) J. R. Stat. Soc. Series B Methodol. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 11
    • 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
  • 12
    • 71849096141 scopus 로고    scopus 로고
    • How does multiple testing correction work?
    • Noble, W. S. (2009) How does multiple testing correction work? Nat. Biotechnol. 27, 1135-1137
    • (2009) Nat. Biotechnol. , vol.27 , pp. 1135-1137
    • Noble, W.S.1
  • 13
    • 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
  • 14
    • 33846567441 scopus 로고    scopus 로고
    • Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy
    • Huttlin, E. L., Hegeman, A. D., Harms, A. C., and Sussman, M. R. (2007) Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy. J. Proteome Res. 6, 392-398
    • (2007) J. Proteome Res. , vol.6 , pp. 392-398
    • Huttlin, E.L.1    Hegeman, A.D.2    Harms, A.C.3    Sussman, M.R.4
  • 15
    • 35748972060 scopus 로고    scopus 로고
    • Semi-supervised learning for peptide identification from shotgun proteomics datasets
    • Kall, L., Canterbury, J. D., Weston, J., Noble, W. S., and MacCoss, M. J. (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4, 923-925
    • (2007) Nat. Methods , vol.4 , pp. 923-925
    • Kall, L.1    Canterbury, J.D.2    Weston, J.3    Noble, W.S.4    Maccoss, M.J.5
  • 16
    • 84864383786 scopus 로고    scopus 로고
    • Bayesian false discovery rates for post-translational modification proteomics
    • Fu, Y. (2012) Bayesian false discovery rates for post-translational modification proteomics. Statistics Interface 5, 47-59
    • (2012) Statistics Interface , vol.5 , pp. 47-59
    • Fu, Y.1
  • 17
    • 77956545752 scopus 로고    scopus 로고
    • Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state-and sequence-dependent scoring
    • Baker, P. R., Medzihradszky, K. F., and Chalkley, R. J. (2010) Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state-and sequence-dependent scoring. Mol. Cell. Proteomics 9, 1795-1803
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 1795-1803
    • Baker, P.R.1    Medzihradszky, K.F.2    Chalkley, R.J.3
  • 19
    • 49749139680 scopus 로고    scopus 로고
    • Simultaneous inference: When should hypothesis testing problems be combined?
    • Efron, B. (2008) Simultaneous inference: When should hypothesis testing problems be combined? Ann. Appl. Stat. 2, 197-223
    • (2008) Ann. Appl. Stat. , vol.2 , pp. 197-223
    • Efron, B.1
  • 20
    • 78649402427 scopus 로고    scopus 로고
    • False discovery rate control with groups
    • Hu, J. X., Zhao, H. Y., and Zhou, H. H. (2010) False discovery rate control with groups. J. Am. Stat. Assoc. 105, 1215-1227
    • (2010) J. Am. Stat. Assoc. , vol.105 , pp. 1215-1227
    • Hu, J.X.1    Zhao, H.Y.2    Zhou, H.H.3
  • 22
    • 33749853607 scopus 로고    scopus 로고
    • A probability-based approach for high-throughput protein phosphorylation analysis and site localization
    • Beausoleil, S. A., Ville?n, J., Gerber, S. A., Rush, J., and Gygi, S. P. (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285-1292
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1285-1292
    • Beausoleil, S.A.1    Villen, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 23
    • 84860879590 scopus 로고    scopus 로고
    • Modification site localization scoring: Strategies and performance
    • Chalkley, R. J., and Clauser, K. R. (2012) Modification site localization scoring: Strategies and performance. Mol. Cell. Proteomics 11, 3-14
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 3-14
    • Chalkley, R.J.1    Clauser, K.R.2
  • 24
    • 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., and Nesvizhskii, A. I. (2008) Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J. Proteome Res. 7, 286-292
    • (2008) J. Proteome Res. , vol.7 , pp. 286-292
    • Choi, H.1    Ghosh, D.2    Nesvizhskii, A.I.3
  • 25
    • 49549099563 scopus 로고    scopus 로고
    • Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry
    • Kall, L., Storey, J. D., and Noble, W. S. (2008) Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics 24, i42-i48
    • (2008) Bioinformatics , vol.24 , pp. 42-48
    • Kall, L.1    Storey, J.D.2    Noble, W.S.3
  • 26
    • 21444449702 scopus 로고    scopus 로고
    • Pfind: A novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry
    • Li, D., Fu, Y., Sun, R., Ling, C., Wei, Y., Zhou, H., Zeng, R., Yang, Q., He, S., and Gao, W. (2005) pFind: A novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry. Bioinformatics 21, 3049-3050
    • (2005) Bioinformatics , vol.21 , pp. 3049-3050
    • Li, D.1    Fu, Y.2    Sun, R.3    Ling, C.4    Wei, Y.5    Zhou, H.6    Zeng, R.7    Yang, Q.8    He, S.9    Gao, W.10
  • 29
    • 79955762105 scopus 로고    scopus 로고
    • DeltAMT: A statistical algorithm for fast detection of protein modifications from LC-MS/MS data
    • Fu, Y., Xiu, L.-Y., Jia, W., Ye, D., Sun, R.-X., Qian, X.-H., and He, S.-M. (2011) DeltAMT: A statistical algorithm for fast detection of protein modifications from LC-MS/MS data. Mol. Cell. Proteomics 10, M110.000455
    • (2011) Mol. Cell. Proteomics , vol.10 , pp. 110000455
    • Fu, Y.1    Xiu, L.-Y.2    Jia, W.3    Ye, D.4    Sun, R.-X.5    Qian, X.-H.6    He, S.-M.7
  • 30
    • 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. X., Wang, H. P., Yuan, Z. F., Chi, H., and He, S. M. (2010) Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. Bioinformatics 26, i399-i406
    • (2010) Bioinformatics , vol.26 , pp. 399-406
    • Ye, D.1    Fu, Y.2    Sun, R.X.3    Wang, H.P.4    Yuan, Z.F.5    Chi, H.6    He, S.M.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.