메뉴 건너뛰기




Volumn 23, Issue 12, 2005, Pages 1562-1567

Identification of post-translational modifications by blind search of mass spectra

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATA ACQUISITION; DATABASE SYSTEMS; PROTEINS;

EID: 28644447919     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1168     Document Type: Article
Times cited : (230)

References (24)
  • 1
    • 2642521977 scopus 로고    scopus 로고
    • Identification of phosphoproteins and their phosphorylation sites in the wehi-231 b lymphoma cell line
    • Shu, H., Chen, S., Bi, Q., Mumby, M. & Brekken, D.L. Identification of phosphoproteins and their phosphorylation sites in the wehi-231 b lymphoma cell line. Mol. Cell. Proteomics 3, 279-286 (2004).
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 279-286
    • Shu, H.1    Chen, S.2    Bi, Q.3    Mumby, M.4    Brekken, D.L.5
  • 2
    • 5644247544 scopus 로고    scopus 로고
    • Strategies for shotgun identification of post-translational modifications by mass spectrometry
    • Cantin, G.T. & Yates, J.R. Strategies for shotgun identification of post-translational modifications by mass spectrometry. J. Chromatogr. A. 1053, 7-14 (2004).
    • (2004) J. Chromatogr. A , vol.1053 , pp. 7-14
    • Cantin, G.T.1    Yates, J.R.2
  • 3
    • 0029645432 scopus 로고
    • Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucteotide databases
    • Yates, J.R., Eng, J.K. & McCormack, A.L. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucteotide databases. Anal. Chem. 67, 3202-3210 (1995).
    • (1995) Anal. Chem. , vol.67 , pp. 3202-3210
    • Yates, J.R.1    Eng, J.K.2    McCormack, A.L.3
  • 4
    • 0034915775 scopus 로고    scopus 로고
    • Mutation-tolerant protein identification by mass spectrometry
    • Pevzner, P.A., Dačík, V. & Tang, C.L. Mutation-tolerant protein identification by mass spectrometry. J. Comput. Biol. 7, 777-787 (2000).
    • (2000) J. Comput. Biol. , vol.7 , pp. 777-787
    • Pevzner, P.A.1    Dačík, V.2    Tang, C.L.3
  • 5
    • 0035107717 scopus 로고    scopus 로고
    • Efficiency of database search for identification of mutated and modified proteins via mass spectrometry
    • Pevzner, P.A., Mulyukov, Z., Dancik, V. & Tang, C.L. Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res. 11, 290-299 (2001).
    • (2001) Genome Res. , vol.11 , pp. 290-299
    • Pevzner, P.A.1    Mulyukov, Z.2    Dancik, V.3    Tang, C.L.4
  • 6
    • 1942423061 scopus 로고    scopus 로고
    • High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results
    • Searle, B.C. et al. High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results. Anal. Chem. 76, 2220-2230 (2004).
    • (2004) Anal. Chem. , vol.76 , pp. 2220-2230
    • Searle, B.C.1
  • 7
    • 22544465253 scopus 로고    scopus 로고
    • SPIDER: Software for protein identification from sequence tags with de novo sequencing error
    • Han, Y., Ma, B. & Zhang, K. SPIDER: software for protein identification from sequence tags with de novo sequencing error. J. Bioinform. Comput. Biol. 3, 697-716 (2005).
    • (2005) J. Bioinform. Comput. Biol. , vol.3 , pp. 697-716
    • Han, Y.1    Ma, B.2    Zhang, K.3
  • 8
    • 17444383114 scopus 로고    scopus 로고
    • P-mod: An algorithm and software to map modifications to peptide sequences using tandem MS data
    • Hansen, B.T., Davey, S.W., Ham, A.J. & Liebler, D.C. P-mod: an algorithm and software to map modifications to peptide sequences using tandem MS data. J. Proteome Res. 4, 358-368 (2005).
    • (2005) J. Proteome Res. , vol.4 , pp. 358-368
    • Hansen, B.T.1    Davey, S.W.2    Ham, A.J.3    Liebler, D.C.4
  • 9
    • 21644461970 scopus 로고    scopus 로고
    • Discovering known and unanticipated protein modifications using MS/MS database searching
    • Tang, W.H. et al. Discovering known and unanticipated protein modifications using MS/MS database searching. Anal. Chem. 77, 3931-3946 (2005).
    • (2005) Anal. Chem. , vol.77 , pp. 3931-3946
    • Tang, W.H.1
  • 10
    • 17444406699 scopus 로고    scopus 로고
    • Identification of protein modifications using MS/MS de now sequencing and the Opensea alignment algorithm
    • Searle, B.S. et al. Identification of protein modifications using MS/MS de now sequencing and the Opensea alignment algorithm. J. Proteome Res. 4, 546-554 (2005).
    • (2005) J. Proteome Res. , vol.4 , pp. 546-554
    • Searle, B.S.1
  • 11
    • 0036828724 scopus 로고    scopus 로고
    • Probability-based validation of protein identifications using a modified SEQUEST algorithm
    • MacCoss, M.J., Wu, C.C. & Yates, J.R. Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 74, 5593-5599 (2002).
    • (2002) Anal. Chem. , vol.74 , pp. 5593-5599
    • MacCoss, M.J.1    Wu, C.C.2    Yates, J.R.3
  • 12
    • 0036406762 scopus 로고    scopus 로고
    • Experimental protein mixture for validating tandem mass spectral analysis
    • Keller, A. et al. Experimental protein mixture for validating tandem mass spectral analysis. OMICS 6, 207-212 (2002).
    • (2002) OMICS , vol.6 , pp. 207-212
    • Keller, A.1
  • 13
    • 27544511899 scopus 로고    scopus 로고
    • Inspect: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra
    • Tanner, S. et al. Inspect: fast and accurate identification of post-translationally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626-4639 (2005).
    • (2005) Anal. Chem. , vol.77 , pp. 4626-4639
    • Tanner, S.1
  • 14
    • 0141955057 scopus 로고    scopus 로고
    • A method for reducing the time required to match protein sequences with tandem mass spectra
    • Craig, R. & Beavis, R.C. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom. 17, 2310-2316 (2003).
    • (2003) Rapid Commun. Mass Spectrom. , vol.17 , pp. 2310-2316
    • Craig, R.1    Beavis, R.C.2
  • 15
    • 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. 67, 1426-1436 (1995).
    • (1995) Anal. Chem. , vol.67 , pp. 1426-1436
    • Yates, J.R.1    Eng, J.K.2    McCormack, A.L.3    Schieltz, D.4
  • 16
    • 0037353846 scopus 로고    scopus 로고
    • Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides
    • Tabb, D.L. et al. Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal. Chem. 75, 1155-1163 (2003).
    • (2003) Anal. Chem. , vol.75 , pp. 1155-1163
    • Tabb, D.L.1
  • 17
    • 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 20, 3551-3567 (1999).
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 18
    • 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. 75, 4646-4658 (2003).
    • (2003) Anal. Chem. , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 19
    • 1842423492 scopus 로고    scopus 로고
    • A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with sequest
    • Razumovskaya, J. et al. A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with sequest. Proteomics 4, 961-969 (2004).
    • (2004) Proteomics , vol.4 , pp. 961-969
    • Razumovskaya, J.1
  • 20
    • 23944455372 scopus 로고    scopus 로고
    • Peptide sequence tags for fast database search in mass-spectrometry
    • Frank, A., Tanner, S.W., Bafna, V. & Pevzner, P.A. Peptide sequence tags for fast database search in mass-spectrometry. J. Proteome Res. 4, 1287-1295 (2005).
    • (2005) J. Proteome Res. , vol.4 , pp. 1287-1295
    • Frank, A.1    Tanner, S.W.2    Bafna, V.3    Pevzner, P.A.4
  • 21
    • 0742305695 scopus 로고    scopus 로고
    • Intensity-based protein identification by protein learning from a library of tandem mass spectra
    • Elias, J.E., Gibbons, F.D., King, O.D., Roth, F.P. & Gygi, S.P. Intensity-based protein identification by protein learning from a library of tandem mass spectra. Nat. Biotechnol. 22, 214-219 (2004).
    • (2004) Nat. Biotechnol. , vol.22 , pp. 214-219
    • Elias, J.E.1    Gibbons, F.D.2    King, O.D.3    Roth, F.P.4    Gygi, S.P.5
  • 22
    • 0037317111 scopus 로고    scopus 로고
    • Intensity-based statistical scorer for tandem mass spectrometry
    • Havilio, M., Haddad, Y. & Smilansky, Z. Intensity-based statistical scorer for tandem mass spectrometry. Anal. Chem. 75, 435-444 (2003).
    • (2003) Anal. Chem. , vol.75 , pp. 435-444
    • Havilio, M.1    Haddad, Y.2    Smilansky, Z.3
  • 23
    • 0042972838 scopus 로고    scopus 로고
    • A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: Support vector machine classification of peptide MS/MS spectra and SEQUEST scores
    • Anderson, D.C., Li, W., Payan, D.G. & W.S., Noble. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res. 2, 137-146 (2003).
    • (2003) J. Proteome Res. , vol.2 , pp. 137-146
    • Anderson, D.C.1    Li, W.2    Payan, D.G.3    Noble, W.S.4
  • 24
    • 7044246160 scopus 로고    scopus 로고
    • Open mass spectrometry search algorithm
    • Geer, L.Y. et al. Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964 (2004).
    • (2004) J. Proteome Res. , vol.3 , pp. 958-964
    • Geer, L.Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.