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Volumn 6, Issue 7, 2007, Pages 1123-1134

Shotgun protein sequencing: Assembly of peptide tandem mass spectra from mixtures of modified proteins

Author keywords

[No Author keywords available]

Indexed keywords

DNA; I KAPPA B KINASE BETA; PROTEINASE; SNAKE VENOM;

EID: 34249780156     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700001-MCP200     Document Type: Article
Times cited : (72)

References (54)
  • 1
    • 0037026512 scopus 로고    scopus 로고
    • Immunology: The roots of antibody diversity
    • Gearhart, P. J. (2002) Immunology: the roots of antibody diversity. Nature 419, 29-31
    • (2002) Nature , vol.419 , pp. 29-31
    • Gearhart, P.J.1
  • 2
    • 33750603695 scopus 로고    scopus 로고
    • Monoclonals - the billion dollar molecules of the future
    • Fall
    • Wiles, M. and Andreassen, P. (2006) Monoclonals - the billion dollar molecules of the future. Drug Discov. World Fall, 17-23
    • (2006) Drug Discov. World , pp. 17-23
    • Wiles, M.1    Andreassen, P.2
  • 3
    • 33745192259 scopus 로고    scopus 로고
    • Recombinant polyclonal antibodies: The next generation of antibody therapeutics?
    • Haurum, J. S. (2006) Recombinant polyclonal antibodies: the next generation of antibody therapeutics? Drug Discov. Today 11, 655-660
    • (2006) Drug Discov. Today , vol.11 , pp. 655-660
    • Haurum, J.S.1
  • 4
    • 0242331757 scopus 로고    scopus 로고
    • Therapeutic potential of venom peptides
    • Lewis, R. J., and Garcia, M. L. (2003) Therapeutic potential of venom peptides. Nat. Rev. Drug Discov. 2, 790-802
    • (2003) Nat. Rev. Drug Discov , vol.2 , pp. 790-802
    • Lewis, R.J.1    Garcia, M.L.2
  • 5
    • 28044453535 scopus 로고    scopus 로고
    • Small peptides, big world: Biotechnological potential in neglected bioactive peptides from arthropod venoms
    • Pimenta, A. M., and De Lima, M. E. (2005) Small peptides, big world: biotechnological potential in neglected bioactive peptides from arthropod venoms. J. Pept. Sci. 11, 670-676
    • (2005) J. Pept. Sci , vol.11 , pp. 670-676
    • Pimenta, A.M.1    De Lima, M.E.2
  • 6
    • 9444231642 scopus 로고    scopus 로고
    • Snake venom prothrombin activators similar to blood coagulation factor Xa
    • Joseph, J. S., and Kini, R. M. (2004) Snake venom prothrombin activators similar to blood coagulation factor Xa. Curr. Drug Targets Cardiovasc. Haematol. Disord. 4, 397-416
    • (2004) Curr. Drug Targets Cardiovasc. Haematol. Disord , vol.4 , pp. 397-416
    • Joseph, J.S.1    Kini, R.M.2
  • 8
    • 0035742118 scopus 로고    scopus 로고
    • Procoagulant proteins from snake venoms
    • Kini, R. M., Rao, V. S., and Joseph, J. S. (2001) Procoagulant proteins from snake venoms. Haemostasis 31, 218-224
    • (2001) Haemostasis , vol.31 , pp. 218-224
    • Kini, R.M.1    Rao, V.S.2    Joseph, J.S.3
  • 9
    • 4444329286 scopus 로고    scopus 로고
    • Intravenous liposomal delivery of the snake venom disintegrin contortrostatin limits breast cancer progression
    • Swenson, S., Costa, F., Minea, R., Sherwin, R. P., Ernst, W., Fujii, G., Yang, D., and Markland, F. S. (2004) Intravenous liposomal delivery of the snake venom disintegrin contortrostatin limits breast cancer progression. Mol. Cancer Ther. 3, 499-511
    • (2004) Mol. Cancer Ther , vol.3 , pp. 499-511
    • Swenson, S.1    Costa, F.2    Minea, R.3    Sherwin, R.P.4    Ernst, W.5    Fujii, G.6    Yang, D.7    Markland, F.S.8
  • 10
    • 0036896057 scopus 로고    scopus 로고
    • Snake venom as therapeutic agents: From toxin to drug development
    • Pal, S. K., Gomes, A., Dasgupta, S. C., and Gomes, A. (2002) Snake venom as therapeutic agents: from toxin to drug development. Indian J. Exp. Biol. 40, 1353-1358
    • (2002) Indian J. Exp. Biol , vol.40 , pp. 1353-1358
    • Pal, S.K.1    Gomes, A.2    Dasgupta, S.C.3    Gomes, A.4
  • 11
    • 0035742117 scopus 로고    scopus 로고
    • A novel snake venom disintegrin that inhibits human ovarian cancer dissemination and angiogenesis in an orthotopic nude mouse model
    • Markland, F. S., Shieh, K., Zhou, Q., Golubkov, V., Sherwin, R. P., Richters, V., and Sposto, R. (2001) A novel snake venom disintegrin that inhibits human ovarian cancer dissemination and angiogenesis in an orthotopic nude mouse model. Haemostasis 31, 183-191
    • (2001) Haemostasis , vol.31 , pp. 183-191
    • Markland, F.S.1    Shieh, K.2    Zhou, Q.3    Golubkov, V.4    Sherwin, R.P.5    Richters, V.6    Sposto, R.7
  • 13
    • 3343003779 scopus 로고    scopus 로고
    • Complete amino acid sequence and phylogenetic analysis of a longchain neurotoxin from the venom of the African banded water cobra, Boulengerina annulata
    • Ogawa, Y., Yanoshita, R., Kuch, U., Samejima, Y., and Mebs, D. (2004) Complete amino acid sequence and phylogenetic analysis of a longchain neurotoxin from the venom of the African banded water cobra, Boulengerina annulata. Toxicon 43, 855-858
    • (2004) Toxicon , vol.43 , pp. 855-858
    • Ogawa, Y.1    Yanoshita, R.2    Kuch, U.3    Samejima, Y.4    Mebs, D.5
  • 14
    • 29344443859 scopus 로고    scopus 로고
    • Conotoxins and the posttranslational modification of secreted gene products
    • Buczek, O., Bulaj, G., and Olivera, B. M. (2005) Conotoxins and the posttranslational modification of secreted gene products. Cell. Mol. Life Sci. 62, 3067-3079
    • (2005) Cell. Mol. Life Sci , vol.62 , pp. 3067-3079
    • Buczek, O.1    Bulaj, G.2    Olivera, B.M.3
  • 15
    • 11244285099 scopus 로고    scopus 로고
    • Electrospray ionization quadrupole time-of-flight and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometric analyses to solve micro-heterogeneity in post-translationally modified peptides from Phoneutria nigriventer (Aranea, Ctenidae) venom
    • Pimenta, A. M., Rates, B., Bloch, C., Gomes, P. C., Santoro, M. M., de Lima, M. E., Richardson, M., and Cordeiro, M. d. N. (2005) Electrospray ionization quadrupole time-of-flight and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometric analyses to solve micro-heterogeneity in post-translationally modified peptides from Phoneutria nigriventer (Aranea, Ctenidae) venom. Rapid Commun. Mass Spectrom. 19, 31-37
    • (2005) Rapid Commun. Mass Spectrom , vol.19 , pp. 31-37
    • Pimenta, A.M.1    Rates, B.2    Bloch, C.3    Gomes, P.C.4    Santoro, M.M.5    de Lima, M.E.6    Richardson, M.7    Cordeiro, M.D.N.8
  • 16
    • 0030030033 scopus 로고    scopus 로고
    • Diet and snake venom evolution
    • Daltry, J. C., Wüster, W., and Thorpe, R. S. (1996) Diet and snake venom evolution. Nature 379, 537-540
    • (1996) Nature , vol.379 , pp. 537-540
    • Daltry, J.C.1    Wüster, W.2    Thorpe, R.S.3
  • 17
    • 33644552124 scopus 로고    scopus 로고
    • Sex-based individual variation of snake venom proteome among eighteen Bothrops jararaca siblings
    • Menezes, M. C., Furtado, M. F., Travaglia-Cardoso, S. R., Camargo, A. C., and Serrano, S. M. (2006) Sex-based individual variation of snake venom proteome among eighteen Bothrops jararaca siblings. Toxicon 47, 304-312
    • (2006) Toxicon , vol.47 , pp. 304-312
    • Menezes, M.C.1    Furtado, M.F.2    Travaglia-Cardoso, S.R.3    Camargo, A.C.4    Serrano, S.M.5
  • 18
    • 28544446184 scopus 로고    scopus 로고
    • Individual venom variability in Crotalus durissus ruruima snakes, a subspecies of Crotalus durissus from the Amazonian region
    • Dos-Santos, M. C., Assis, E. B., Moreira, T. D., Pinheiro, J., and Fortes-Dias, C. L. (2005) Individual venom variability in Crotalus durissus ruruima snakes, a subspecies of Crotalus durissus from the Amazonian region. Toxicon 46, 958-961
    • (2005) Toxicon , vol.46 , pp. 958-961
    • Dos-Santos, M.C.1    Assis, E.B.2    Moreira, T.D.3    Pinheiro, J.4    Fortes-Dias, C.L.5
  • 19
    • 33646138940 scopus 로고    scopus 로고
    • Mass spectrometry in toxinology: A 21st-century technology for the study of biopolymers from venoms
    • Escoubas, P. (2006) Mass spectrometry in toxinology: a 21st-century technology for the study of biopolymers from venoms. Toxicon 47, 609-613
    • (2006) Toxicon , vol.47 , pp. 609-613
    • Escoubas, P.1
  • 20
    • 33646152321 scopus 로고    scopus 로고
    • Comparison of indirect and direct approaches using ion-trap and Fourier transform ion cyclotron resonance mass spectrometry for exploring viperid venom proteomes
    • Fox, J. W., Ma, L., Nelson, K., Sherman, N. E., and Serrano, S. M. (2006) Comparison of indirect and direct approaches using ion-trap and Fourier transform ion cyclotron resonance mass spectrometry for exploring viperid venom proteomes. Toxicon 47, 700-714
    • (2006) Toxicon , vol.47 , pp. 700-714
    • Fox, J.W.1    Ma, L.2    Nelson, K.3    Sherman, N.E.4    Serrano, S.M.5
  • 21
    • 20444438029 scopus 로고    scopus 로고
    • Scares, M,. R., Oliveira-Carvalho, A. L., Wermelinger, L. S., Zingali, R. B., Ho, P. L., Junqueira-de Azevedo, I. d. L., and Diniz, M. R. (2005) Identification of novel bradykinin-potentiating peptides and C-type natriuretic peptide from Lachesis muta venom. Toxicon 46, 31-38
    • Scares, M,. R., Oliveira-Carvalho, A. L., Wermelinger, L. S., Zingali, R. B., Ho, P. L., Junqueira-de Azevedo, I. d. L., and Diniz, M. R. (2005) Identification of novel bradykinin-potentiating peptides and C-type natriuretic peptide from Lachesis muta venom. Toxicon 46, 31-38
  • 22
    • 20644445645 scopus 로고    scopus 로고
    • Fast analysis of low molecular mass compounds present in snake venom: Identification of ten new pyroglutamate-containing peptides
    • Wermelinger, L. S., Dutra, D. L., Oliveira-Carvalho, A. L., Scares, M. R., Bloch, C., and Zingali, R. B. (2005) Fast analysis of low molecular mass compounds present in snake venom: identification of ten new pyroglutamate-containing peptides. Rapid Commun. Mass Spectrom. 19, 1703-1708
    • (2005) Rapid Commun. Mass Spectrom , vol.19 , pp. 1703-1708
    • Wermelinger, L.S.1    Dutra, D.L.2    Oliveira-Carvalho, A.L.3    Scares, M.R.4    Bloch, C.5    Zingali, R.B.6
  • 24
    • 0034814613 scopus 로고    scopus 로고
    • A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry
    • Chen, T., Kao, M. Y., Tepel, M., Rush, J., and Church, G. M. (2001) A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 8, 325-337
    • (2001) J. Comput. Biol , vol.8 , pp. 325-337
    • Chen, T.1    Kao, M.Y.2    Tepel, M.3    Rush, J.4    Church, G.M.5
  • 26
    • 0023143159 scopus 로고
    • The primary structure of thioredoxin from Chromatium vinosum determined by high-performance tandem mass spectrometry
    • Johnson, R. S., and Biemann, K. (1987) The primary structure of thioredoxin from Chromatium vinosum determined by high-performance tandem mass spectrometry. Biochemistry 26, 1209-1214
    • (1987) Biochemistry , vol.26 , pp. 1209-1214
    • Johnson, R.S.1    Biemann, K.2
  • 28
    • 10644292740 scopus 로고    scopus 로고
    • Shotgun protein sequencing by tandem mass spectra assembly
    • Bandeira, N., Tang, H., Bafna, V., and Pevzner, P. (2004) Shotgun protein sequencing by tandem mass spectra assembly. Anal. Chem. 76, 7221-7233
    • (2004) Anal. Chem , vol.76 , pp. 7221-7233
    • Bandeira, N.1    Tang, H.2    Bafna, V.3    Pevzner, P.4
  • 29
    • 33644856320 scopus 로고    scopus 로고
    • Effects of modified digestion schemes on the identification of proteins from complex mixtures
    • Klammer, A. A., and MacCoss, M. J. (2006) Effects of modified digestion schemes on the identification of proteins from complex mixtures. J. Proteome Res. 5, 695-700
    • (2006) J. Proteome Res , vol.5 , pp. 695-700
    • Klammer, A.A.1    MacCoss, M.J.2
  • 32
    • 23744446773 scopus 로고    scopus 로고
    • Vinson, 32 J. P., Jaffe, D. B., O'Neill, K., Karlsson, E. K., Stange-Thomann, N., Anderson, S., Mesirov, J. P., Satoh, N., Satou, Y., Nusbaum, C., Birren, B., Galagan, J. E., and Lander, E. S. (2005) Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res. 15, 1127-1135
    • Vinson, 32 J. P., Jaffe, D. B., O'Neill, K., Karlsson, E. K., Stange-Thomann, N., Anderson, S., Mesirov, J. P., Satoh, N., Satou, Y., Nusbaum, C., Birren, B., Galagan, J. E., and Lander, E. S. (2005) Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res. 15, 1127-1135
  • 33
    • 33745800431 scopus 로고    scopus 로고
    • Bandeira, N., Tsur, D., Frank, A., and Pevzner, P. A. (2006) A new approach to protein identification, in Proceeding of the Tenth Annual International Conference in Research in Computational Molecular Biology (RECOMB 2006) (Apostolico, A., Guerra, C., Istrail, S., Pevzner, P. A., and Waterman, M., eds) 3909, pp. 363-378, Springer, Germany
    • Bandeira, N., Tsur, D., Frank, A., and Pevzner, P. A. (2006) A new approach to protein identification, in Proceeding of the Tenth Annual International Conference in Research in Computational Molecular Biology (RECOMB 2006) (Apostolico, A., Guerra, C., Istrail, S., Pevzner, P. A., and Waterman, M., eds) Vol. 3909, pp. 363-378, Springer, Germany
  • 35
    • 4644275238 scopus 로고    scopus 로고
    • De novo repeat classification and fragment assembly
    • Pevzner, P. A., Tang, H., and Tesler, G. (2004) De novo repeat classification and fragment assembly. Genome Res. 14, 1786-1796
    • (2004) Genome Res , vol.14 , pp. 1786-1796
    • Pevzner, P.A.1    Tang, H.2    Tesler, G.3
  • 36
    • 0029105096 scopus 로고
    • Molecular cloning and expression of catrocollastatin, a snake venom protein from Crotalus atrox (western diamondback rattlesnake) which inhibits platelet adhesion to collagen
    • Zhou, O., Smith, J. B., and Grossman, M. H. (1995) Molecular cloning and expression of catrocollastatin, a snake venom protein from Crotalus atrox (western diamondback rattlesnake) which inhibits platelet adhesion to collagen. Biochem. J. 307, 411-417
    • (1995) Biochem. J , vol.307 , pp. 411-417
    • Zhou, O.1    Smith, J.B.2    Grossman, M.H.3
  • 37
    • 0035965199 scopus 로고    scopus 로고
    • Complete reconstitution of human IκB kinase (IKK) complex in yeast. Assessment of its stolchiometry and the le of IKKγ on the complex activity in the absence of stimulation
    • Miller, B. S., and Zandi, E. (2001) Complete reconstitution of human IκB kinase (IKK) complex in yeast. Assessment of its stolchiometry and the le of IKKγ on the complex activity in the absence of stimulation. J. Biol. Chem. 276, 36320-36326
    • (2001) J. Biol. Chem , vol.276 , pp. 36320-36326
    • Miller, B.S.1    Zandi, E.2
  • 38
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • Tanner, S., Shu, H., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., and Bafna, V. (2005) InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 77, 4626-4639
    • (2005) Anal. Chem , vol.77 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 39
    • 85047687595 scopus 로고    scopus 로고
    • Role of lκB kinase in tumorigenesis
    • Hu, M. C., and Hung, M. C. (2005) Role of lκB kinase in tumorigenesis. Future Oncol. 1, 67-78
    • (2005) Future Oncol , vol.1 , pp. 67-78
    • Hu, M.C.1    Hung, M.C.2
  • 40
    • 28644447919 scopus 로고    scopus 로고
    • Identification of post-translational modifications by blind search of mass spectra
    • Tsur, D., Tanner, S., Zandi, E., Bafna, V., and Pevzner, P. A. (2005) Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol. 23, 1562-1567
    • (2005) Nat Biotechnol , vol.23 , pp. 1562-1567
    • Tsur, D.1    Tanner, S.2    Zandi, E.3    Bafna, V.4    Pevzner, P.A.5
  • 41
    • 0036523742 scopus 로고    scopus 로고
    • Cyclization of N-terminal S-carbamoylmethylcysteine causing loss of 17 Da from peptides and extra peaks in peptide maps
    • Geoghegan, K. F., Hoth, L. R., Tan, D. H., Borzilleri, K. A., Withka, J. M., and Boyd, J. G. (2002) Cyclization of N-terminal S-carbamoylmethylcysteine causing loss of 17 Da from peptides and extra peaks in peptide maps. J. Proteome Res. 1, 181-187
    • (2002) J. Proteome Res , vol.1 , pp. 181-187
    • Geoghegan, K.F.1    Hoth, L.R.2    Tan, D.H.3    Borzilleri, K.A.4    Withka, J.M.5    Boyd, J.G.6
  • 42
    • 13844319908 scopus 로고    scopus 로고
    • PepNovo: De Novo peptide sequencing via probabilistic network modeling
    • Frank, A., and Pevzner, P. (2005) PepNovo: de Novo peptide sequencing via probabilistic network modeling. Anal. Chem. 77, 964-973
    • (2005) Anal. Chem , vol.77 , pp. 964-973
    • Frank, A.1    Pevzner, P.2
  • 43
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T. F., and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197
    • (1981) J. Mol. Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 44
    • 8844287599 scopus 로고    scopus 로고
    • Current chemical tagging strategies for proteome analysis by mass spectrometry
    • Leitner, A., and Lindner, W. (2004) Current chemical tagging strategies for proteome analysis by mass spectrometry. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 813, 1-26
    • (2004) J. Chromatogr. B Anal. Technol. Biomed. Life Sci , vol.813 , pp. 1-26
    • Leitner, A.1    Lindner, W.2
  • 45
    • 26444456180 scopus 로고    scopus 로고
    • Application of mass spectrometry in proteomics
    • Guerrera, I. C., and Kleiner, O. (2005) Application of mass spectrometry in proteomics. Biosci. Rep. 25, 71-93
    • (2005) Biosci. Rep , vol.25 , pp. 71-93
    • Guerrera, I.C.1    Kleiner, O.2
  • 47
    • 0029312158 scopus 로고
    • Toward simplifying and accurately formulating fragment assembly
    • Myers, E. W. (1995) Toward simplifying and accurately formulating fragment assembly. J. Comput. Biol. 2, 275-290
    • (1995) J. Comput. Biol , vol.2 , pp. 275-290
    • Myers, E.W.1
  • 48
    • 0025038664 scopus 로고
    • Fast algorithm for peptide sequencing by mass spectroscopy
    • Bartels, C. (1990) Fast algorithm for peptide sequencing by mass spectroscopy. Biomed. Environ. Mass Spectrom. 19, 363-368
    • (1990) Biomed. Environ. Mass Spectrom , vol.19 , pp. 363-368
    • Bartels, C.1
  • 50
    • 22544465253 scopus 로고    scopus 로고
    • SPIDER: Software for protein identification from sequence tags with de novo sequencing error
    • Han, Y., Ma, B., and Zhang, K. (2005) SPIDER: software for protein identification from sequence tags with de novo sequencing error. J. Bioinform. Comput. Biol. 3, 697-716
    • (2005) J. Bioinform. Comput. Biol , vol.3 , pp. 697-716
    • Han, Y.1    Ma, B.2    Zhang, K.3
  • 52
    • 33845960314 scopus 로고    scopus 로고
    • How to discriminate between leucine and isoleucine by low energy ESI-trap MSn
    • Armirotti, A., Millo, E., and Damonte, G. (2007) How to discriminate between leucine and isoleucine by low energy ESI-trap MSn. J. Am. Soc. Mass Spectrom. 18, 57-63
    • (2007) J. Am. Soc. Mass Spectrom , vol.18 , pp. 57-63
    • Armirotti, A.1    Millo, E.2    Damonte, G.3
  • 53
  • 54
    • 0034915775 scopus 로고    scopus 로고
    • Mutation-tolerant protein identification by mass spectrometry
    • Pevzner, P. A., Dancik, V., and Tang, C. L. (2000) Mutation-tolerant protein identification by mass spectrometry. J. Comput. Biol. 7, 777-787
    • (2000) J. Comput. Biol , vol.7 , pp. 777-787
    • Pevzner, P.A.1    Dancik, V.2    Tang, C.L.3


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