메뉴 건너뛰기




Volumn 73, Issue 11, 2010, Pages 2124-2135

Proteogenomics to discover the full coding content of genomes: A computational perspective

Author keywords

Gene annotation; Mass spectrometry; Proteogenomics

Indexed keywords

PEPTIDE;

EID: 77957237701     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2010.06.007     Document Type: Review
Times cited : (137)

References (95)
  • 1
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng J., McCormack A., Yates J. 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, J.1    McCormack, A.2    Yates, J.3
  • 4
    • 44349191457 scopus 로고    scopus 로고
    • Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
    • Campbell P.J., Stephens P.J., Pleasance E.D., O'Meara S., Li H., Santarius T., et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008, 40:722-729.
    • (2008) Nat Genet , vol.40 , pp. 722-729
    • Campbell, P.J.1    Stephens, P.J.2    Pleasance, E.D.3    O'Meara, S.4    Li, H.5    Santarius, T.6
  • 5
    • 0030457112 scopus 로고    scopus 로고
    • Programmed translational frameshifting
    • Farabaugh P.J. Programmed translational frameshifting. Annu Rev Genet 1996, 30:507-528.
    • (1996) Annu Rev Genet , vol.30 , pp. 507-528
    • Farabaugh, P.J.1
  • 8
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1 of the human genome by the ENCODE pilot project
    • Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., et al. Identification and analysis of functional elements in 1 of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3    Guigo, R.4    Gingeras, T.R.5    Margulies, E.H.6
  • 9
    • 0035180589 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant
    • Huala E., Dickerman A.W., Garcia-Hernandez M., Weems D., Reiser L., LaFond F., et al. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 2001, 29:102-105.
    • (2001) Nucleic Acids Res , vol.29 , pp. 102-105
    • Huala, E.1    Dickerman, A.W.2    Garcia-Hernandez, M.3    Weems, D.4    Reiser, L.5    LaFond, F.6
  • 10
    • 34250857552 scopus 로고    scopus 로고
    • Genomics DNA study forces rethink of what it means to be a gene
    • Pennisi E. Genomics DNA study forces rethink of what it means to be a gene. Science 2007, 316:1556-1557.
    • (2007) Science , vol.316 , pp. 1556-1557
    • Pennisi, E.1
  • 11
    • 37249005195 scopus 로고    scopus 로고
    • Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    • Brent M.R. Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet 2008, 9:62-73.
    • (2008) Nat Rev Genet , vol.9 , pp. 62-73
    • Brent, M.R.1
  • 12
    • 34548452940 scopus 로고    scopus 로고
    • Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation
    • Gupta N., Tanner S., Jaitly N., Adkins J.N., Lipton M., Edwards R., et al. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res 2007, 17:1362-1377.
    • (2007) Genome Res , vol.17 , pp. 1362-1377
    • Gupta, N.1    Tanner, S.2    Jaitly, N.3    Adkins, J.N.4    Lipton, M.5    Edwards, R.6
  • 13
    • 0035036534 scopus 로고    scopus 로고
    • Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
    • Kan Z., Rouchka E.C., Gish W.R., States D.J. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 2001, 11:889-900.
    • (2001) Genome Res , vol.11 , pp. 889-900
    • Kan, Z.1    Rouchka, E.C.2    Gish, W.R.3    States, D.J.4
  • 15
    • 37648999313 scopus 로고    scopus 로고
    • Distinguishing protein-coding and noncoding genes in the human genome
    • Clamp M., Fry B., Kamal M., Xie X., Cuff J., Lin M.F., et al. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 2007, 104:19428-19433.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 19428-19433
    • Clamp, M.1    Fry, B.2    Kamal, M.3    Xie, X.4    Cuff, J.5    Lin, M.F.6
  • 16
    • 0036796369 scopus 로고    scopus 로고
    • Current methods of gene prediction, their strengths and weaknesses
    • Mathe C., Sagot M.F., Schiex T., Rouze P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 2002, 30:4103-4117.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4103-4117
    • Mathe, C.1    Sagot, M.F.2    Schiex, T.3    Rouze, P.4
  • 18
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94.
    • (1997) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 19
    • 0029645432 scopus 로고
    • Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
    • Yates J.R., Eng J.K., McCormack A.L. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem 1995, 67:3202-3210.
    • (1995) Anal Chem , vol.67 , pp. 3202-3210
    • Yates, J.R.1    Eng, J.K.2    McCormack, A.L.3
  • 20
    • 0037422575 scopus 로고    scopus 로고
    • Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans
    • Lewis B.P., Green R.E., Brenner S.E. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci USA 2003, 100:189-192.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 189-192
    • Lewis, B.P.1    Green, R.E.2    Brenner, S.E.3
  • 22
    • 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
  • 23
    • 67651173106 scopus 로고    scopus 로고
    • Proteomics by mass spectrometry: approaches, advances, and applications
    • Yates J.R., Ruse C.I., Nakorchevsky A. Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng 2009, 11:49-79.
    • (2009) Annu Rev Biomed Eng , vol.11 , pp. 49-79
    • Yates, J.R.1    Ruse, C.I.2    Nakorchevsky, A.3
  • 26
    • 0032509302 scopus 로고    scopus 로고
    • Sequencing consortium, genome sequence of the nematode C. elegans: a platform for investigating biology
    • elegans C. Sequencing consortium, genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998, 282:2012-2018.
    • (1998) Science , vol.282 , pp. 2012-2018
    • elegans, C.1
  • 27
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Initiative T.A.G. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
    • (2000) Nature , vol.408 , pp. 796-815
    • Initiative, T.A.G.1
  • 33
    • 25444475024 scopus 로고    scopus 로고
    • Genome annotation of Anopheles gambiae using mass spectrometry-derived data
    • Kalume D.E., Peri S., Reddy R., Zhong J., Okulate M., Kumar N., et al. Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics 2005, 6:128.
    • (2005) BMC Genomics , vol.6 , pp. 128
    • Kalume, D.E.1    Peri, S.2    Reddy, R.3    Zhong, J.4    Okulate, M.5    Kumar, N.6
  • 35
    • 33846884410 scopus 로고    scopus 로고
    • Improving gene annotation using peptide mass spectrometry
    • Tanner S., Shen Z., Ng J., Florea L., Guigo R., Briggs S.P., et al. Improving gene annotation using peptide mass spectrometry. Genome Res 2007, 17:231-239.
    • (2007) Genome Res , vol.17 , pp. 231-239
    • Tanner, S.1    Shen, Z.2    Ng, J.3    Florea, L.4    Guigo, R.5    Briggs, S.P.6
  • 38
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
    • (2001) Nat Biotechnol , vol.19 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates, J.R.3
  • 39
    • 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 1999, 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
  • 40
    • 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., Gygi S.P. 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    Gygi, S.P.5
  • 41
    • 30744444934 scopus 로고    scopus 로고
    • PepHMM: a hidden Markov model based scoring function for mass spectrometry database search
    • Wan Y., Yang A., Chen T. PepHMM: a hidden Markov model based scoring function for mass spectrometry database search. Anal Chem 2006, 78:432-437.
    • (2006) Anal Chem , vol.78 , pp. 432-437
    • Wan, Y.1    Yang, A.2    Chen, T.3
  • 42
    • 33847234661 scopus 로고    scopus 로고
    • Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry
    • Bern M., Cai Y., Goldberg D. Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. Anal Chem 2007, 79:1393-1400.
    • (2007) Anal Chem , vol.79 , pp. 1393-1400
    • Bern, M.1    Cai, Y.2    Goldberg, D.3
  • 43
    • 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., Noble W.S. 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    Noble, W.S.5
  • 44
    • 66749129629 scopus 로고    scopus 로고
    • A ranking-based scoring function for peptide-spectrum matches
    • Frank A.M. A ranking-based scoring function for peptide-spectrum matches. J Proteome Res 2009, 8:2241-2252.
    • (2009) J Proteome Res , vol.8 , pp. 2241-2252
    • Frank, A.M.1
  • 45
    • 66749169317 scopus 로고    scopus 로고
    • Predicting intensity ranks of peptide fragment ions
    • Frank A.M. Predicting intensity ranks of peptide fragment ions. J Proteome Res 2009, 8:2226-2240.
    • (2009) J Proteome Res , vol.8 , pp. 2226-2240
    • Frank, A.M.1
  • 46
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • 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.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 47
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias J.E., Gygi S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4:207-214.
    • (2007) Nat Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 49
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
    • Kim S., Gupta N., Pevzner P.A. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res 2008, 7:3354-3363.
    • (2008) J Proteome Res , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 50
    • 52949154317 scopus 로고    scopus 로고
    • Statistical characterization of a 1D random potential problem - with applications in score statistics of MS-based peptide sequencing
    • Alves G., Yu Y.K. Statistical characterization of a 1D random potential problem - with applications in score statistics of MS-based peptide sequencing. Physica A 2008, 387:6538-6544.
    • (2008) Physica A , vol.387 , pp. 6538-6544
    • Alves, G.1    Yu, Y.K.2
  • 51
    • 33745054329 scopus 로고    scopus 로고
    • Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
    • Fermin D., Allen B.B., Blackwell T.W., Menon R., Adamski M., Xu Y., et al. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 2006, 7:R35.
    • (2006) Genome Biol , vol.7
    • Fermin, D.1    Allen, B.B.2    Blackwell, T.W.3    Menon, R.4    Adamski, M.5    Xu, Y.6
  • 52
    • 70149084269 scopus 로고    scopus 로고
    • Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
    • Grobei M.A., Qeli E., Brunner E., Rehrauer H., Zhang R., Roschitzki B., et al. Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function. Genome Res 2009, 19:1786-1800.
    • (2009) Genome Res , vol.19 , pp. 1786-1800
    • Grobei, M.A.1    Qeli, E.2    Brunner, E.3    Rehrauer, H.4    Zhang, R.5    Roschitzki, B.6
  • 53
    • 0942287072 scopus 로고    scopus 로고
    • Proteogenomic mapping as a complementary method to perform genome annotation
    • Jaffe J.D., Berg H.C., Church G.M. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 2004, 4:59-77.
    • (2004) Proteomics , vol.4 , pp. 59-77
    • Jaffe, J.D.1    Berg, H.C.2    Church, G.M.3
  • 54
    • 20144381803 scopus 로고    scopus 로고
    • Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    • Desiere F., Deutsch E.W., Nesvizhskii A.I., Mallick P., King N.L., Eng J.K., et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol 2005, 6:R9.
    • (2005) Genome Biol , vol.6
    • Desiere, F.1    Deutsch, E.W.2    Nesvizhskii, A.I.3    Mallick, P.4    King, N.L.5    Eng, J.K.6
  • 55
    • 34247254351 scopus 로고    scopus 로고
    • Novel peptide identification from tandem mass spectra using ESTs and sequence database compression
    • Edwards N.J. Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol Syst Biol 2007, 3:102.
    • (2007) Mol Syst Biol , vol.3 , pp. 102
    • Edwards, N.J.1
  • 58
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamov A.A., Solovyev V.V. Ab initio gene finding in Drosophila genomic DNA. Genome Res 2000, 10:516-522.
    • (2000) Genome Res , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 59
    • 33645161645 scopus 로고    scopus 로고
    • Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    • Stanke M., Schoffmann O., Morgenstern B., Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinform 2006, 7:62.
    • (2006) BMC Bioinform , vol.7 , pp. 62
    • Stanke, M.1    Schoffmann, O.2    Morgenstern, B.3    Waack, S.4
  • 61
    • 0035350894 scopus 로고    scopus 로고
    • Mass spectrometry allows direct identification of proteins in large genomes
    • Kuster B., Mortensen P., Andersen J.S., Mann M. Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 2001, 1:641-650.
    • (2001) Proteomics , vol.1 , pp. 641-650
    • Kuster, B.1    Mortensen, P.2    Andersen, J.S.3    Mann, M.4
  • 62
    • 84872976442 scopus 로고    scopus 로고
    • The 1000 genome project
    • The 1000 genome project.
  • 65
    • 0035346719 scopus 로고    scopus 로고
    • Interrogating the human genome using uninterpreted mass spectrometry data
    • Choudhary J.S., Blackstock W.P., Creasy D.M., Cottrell J.S. Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics 2001, 1:651-667.
    • (2001) Proteomics , vol.1 , pp. 651-667
    • Choudhary, J.S.1    Blackstock, W.P.2    Creasy, D.M.3    Cottrell, J.S.4
  • 66
    • 24744455665 scopus 로고    scopus 로고
    • Automatic quality assessment of peptide tandem mass spectra
    • Bern M., Goldberg D., McDonald W.H., Yates J.R. Automatic quality assessment of peptide tandem mass spectra. Bioinformatics 2004, 20(Suppl 1):49-54.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1 , pp. 49-54
    • Bern, M.1    Goldberg, D.2    McDonald, W.H.3    Yates, J.R.4
  • 67
    • 33645708138 scopus 로고    scopus 로고
    • Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
    • Nesvizhskii A.I., Roos F.F., Grossmann J., Vogelzang M., Eddes J.S., Gruissem W., et al. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics 2006, 5:652-670.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 652-670
    • Nesvizhskii, A.I.1    Roos, F.F.2    Grossmann, J.3    Vogelzang, M.4    Eddes, J.S.5    Gruissem, W.6
  • 69
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: matching proteins with tandem mass spectra
    • Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 70
    • 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., 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    Zandi, E.5    Mumby, M.6
  • 71
    • 28644447919 scopus 로고    scopus 로고
    • Identification of post-translational modifications by blind search of mass spectra
    • Tsur D., Tanner S., Zandi E., Bafna V., Pevzner P.A. Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol 2005, 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
  • 72
    • 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 2003, 75:4646-4658.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 74
    • 53549100731 scopus 로고    scopus 로고
    • Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
    • Merrihew G.E., Davis C., Ewing B., Williams G., Kall L., Frewen B.E., et al. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res 2008, 18:1660-1669.
    • (2008) Genome Res , vol.18 , pp. 1660-1669
    • Merrihew, G.E.1    Davis, C.2    Ewing, B.3    Williams, G.4    Kall, L.5    Frewen, B.E.6
  • 75
    • 76649085822 scopus 로고    scopus 로고
    • Proteomic-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons
    • M. Baudet, et al., Proteomic-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons, Mol. Cell Proteomics.
    • Mol. Cell Proteomics
    • Baudet, M.1
  • 76
    • 23744515352 scopus 로고    scopus 로고
    • Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias
    • Wang R., Prince J.T., Marcotte E.M. Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res 2005, 15:1118-1126.
    • (2005) Genome Res , vol.15 , pp. 1118-1126
    • Wang, R.1    Prince, J.T.2    Marcotte, E.M.3
  • 77
    • 0037015610 scopus 로고    scopus 로고
    • Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry
    • Lasonder E., Ishihama Y., Andersen J.S., Vermunt A.M., Pain A., Sauerwein R.W., et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 2002, 419:537-542.
    • (2002) Nature , vol.419 , pp. 537-542
    • Lasonder, E.1    Ishihama, Y.2    Andersen, J.S.3    Vermunt, A.M.4    Pain, A.5    Sauerwein, R.W.6
  • 78
    • 63549124859 scopus 로고    scopus 로고
    • Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti
    • de Groot A., Dulermo R., Ortet P., Blanchard L., Guerin P., Fernandez B., et al. Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet 2009, 5:e1000434.
    • (2009) PLoS Genet , vol.5
    • de Groot, A.1    Dulermo, R.2    Ortet, P.3    Blanchard, L.4    Guerin, P.5    Fernandez, B.6
  • 79
    • 61449116914 scopus 로고    scopus 로고
    • Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol
    • Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.M., Van Dorsselaer A., et al. Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res 2009, 19:128-135.
    • (2009) Genome Res , vol.19 , pp. 128-135
    • Gallien, S.1    Perrodou, E.2    Carapito, C.3    Deshayes, C.4    Reyrat, J.M.5    Van Dorsselaer, A.6
  • 80
    • 43749090090 scopus 로고    scopus 로고
    • Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes
    • Gupta N., Benhamida J., Bhargava V., Goodman D., Kain E., Kerman I., et al. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res 2008, 18:1133-1142.
    • (2008) Genome Res , vol.18 , pp. 1133-1142
    • Gupta, N.1    Benhamida, J.2    Bhargava, V.3    Goodman, D.4    Kain, E.5    Kerman, I.6
  • 81
    • 34247375985 scopus 로고    scopus 로고
    • Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry
    • Asara J.M., Schweitzer M.H., Freimark L.M., Phillips M., Cantley L.C. Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 2007, 316:280-285.
    • (2007) Science , vol.316 , pp. 280-285
    • Asara, J.M.1    Schweitzer, M.H.2    Freimark, L.M.3    Phillips, M.4    Cantley, L.C.5
  • 83
    • 37849018459 scopus 로고    scopus 로고
    • Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
    • [author reply 33]
    • Buckley M., Walker A., Ho S.Y., Yang Y., Smith C., Ashton P., et al. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science 2008, 319:33. [author reply 33].
    • (2008) Science , vol.319 , pp. 33
    • Buckley, M.1    Walker, A.2    Ho, S.Y.3    Yang, Y.4    Smith, C.5    Ashton, P.6
  • 84
    • 50149116038 scopus 로고    scopus 로고
    • Comment on "protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
    • [author reply 1040]
    • Pevzner P.A., Kim S., Ng J. Comment on "protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science 2008, 321:1040. [author reply 1040].
    • (2008) Science , vol.321 , pp. 1040
    • Pevzner, P.A.1    Kim, S.2    Ng, J.3
  • 85
    • 0035326344 scopus 로고    scopus 로고
    • Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching
    • Shevchenko A., Sunyaev S., Loboda A., Shevchenko A., Bork P., Ens W., et al. Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal Chem 2001, 73:1917-1926.
    • (2001) Anal Chem , vol.73 , pp. 1917-1926
    • Shevchenko, A.1    Sunyaev, S.2    Loboda, A.3    Shevchenko, A.4    Bork, P.5    Ens, W.6
  • 86
    • 58149307960 scopus 로고    scopus 로고
    • Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach
    • Na S., Jeong J., Park H., Lee K.J., Paek E. Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach. Mol Cell Proteomics 2008, 7:2452-2463.
    • (2008) Mol Cell Proteomics , vol.7 , pp. 2452-2463
    • Na, S.1    Jeong, J.2    Park, H.3    Lee, K.J.4    Paek, E.5
  • 87
    • 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 2005, 3:697-716.
    • (2005) J Bioinform Comput Biol , vol.3 , pp. 697-716
    • Han, Y.1    Ma, B.2    Zhang, K.3
  • 89
    • 57449097186 scopus 로고    scopus 로고
    • Automated de novo protein sequencing of monoclonal antibodies
    • Bandeira N., Pham V., Pevzner P., Arnott D., Lill J.R. Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol 2008, 26:1336-1338.
    • (2008) Nat Biotechnol , vol.26 , pp. 1336-1338
    • Bandeira, N.1    Pham, V.2    Pevzner, P.3    Arnott, D.4    Lill, J.R.5
  • 90
    • 69949152299 scopus 로고    scopus 로고
    • Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
    • Liu X., Han Y., Yuen D., Ma B. Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy. Bioinformatics 2009, 25:2174-2180.
    • (2009) Bioinformatics , vol.25 , pp. 2174-2180
    • Liu, X.1    Han, Y.2    Yuen, D.3    Ma, B.4
  • 91
    • 77953155288 scopus 로고    scopus 로고
    • Template proteogenomics: sequencing whole proteins using an imperfect database
    • Castellana N.E., Pham V., Arnott D., Lill J.R., Bafna V. Template proteogenomics: sequencing whole proteins using an imperfect database. Mol Cell Proteomics 2010, 9:1260-1270.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 1260-1270
    • Castellana, N.E.1    Pham, V.2    Arnott, D.3    Lill, J.R.4    Bafna, V.5
  • 93
    • 33847177982 scopus 로고    scopus 로고
    • Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract
    • Klaassens E.S., de Vos W.M., Vaughan E.E. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl Environ Microbiol 2007, 73:1388-1392.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 1388-1392
    • Klaassens, E.S.1    de Vos, W.M.2    Vaughan, E.E.3
  • 95
    • 3242878999 scopus 로고    scopus 로고
    • PrediSi: prediction of signal peptides and their cleavage positions
    • Hiller K., Grote A., Scheer M., Munch R., Jahn D. PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res 2004, 32:W375-379.
    • (2004) Nucleic Acids Res , vol.32
    • Hiller, K.1    Grote, A.2    Scheer, M.3    Munch, R.4    Jahn, D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.