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Volumn 18, Issue 7, 2008, Pages 1133-1142

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENETICS; DNA SEQUENCE; GENOME ANALYSIS; GENOMICS; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; SHEWANELLA;

EID: 43749090090     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.074344.107     Document Type: Article
Times cited : (91)

References (57)
  • 3
    • 0033861549 scopus 로고    scopus 로고
    • Human and mouse gene structure: Comparative analysis and application to exon prediction
    • Batzoglou, S., Pachter, L., Mesirov, J., Berger, B., and Lander, E. 2000. Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Res. 10: 950-958.
    • (2000) Genome Res , vol.10 , pp. 950-958
    • Batzoglou, S.1    Pachter, L.2    Mesirov, J.3    Berger, B.4    Lander, E.5
  • 4
    • 0023135722 scopus 로고
    • Processing of the initiation methionine from proteins: Properties of the Escherichia coli methionine aminopeptidase and its gene structure
    • Ben-Bassat, A., Bauer, K., Chang, S., Myambo, K., Boosman, A., and Chang, S. 1987. Processing of the initiation methionine from proteins: Properties of the Escherichia coli methionine aminopeptidase and its gene structure. J. Bacteriol. 169: 751-757.
    • (1987) J. Bacteriol , vol.169 , pp. 751-757
    • Ben-Bassat, A.1    Bauer, K.2    Chang, S.3    Myambo, K.4    Boosman, A.5    Chang, S.6
  • 5
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • Bendtsen, J., Nielsen, H., von Heijne, G., and Brunak, S. 2004. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340: 783-795.
    • (2004) J. Mol. Biol , vol.340 , pp. 783-795
    • Bendtsen, J.1    Nielsen, H.2    von Heijne, G.3    Brunak, S.4
  • 6
    • 33646907086 scopus 로고    scopus 로고
    • Reporting protein identification data: The next generation of guidelines
    • Bradshaw, R., Burlingame, A., Carr, S., and Aebersold, R. 2006. Reporting protein identification data: The next generation of guidelines. Mol. Cell. Proteomics 5: 787-788.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 787-788
    • Bradshaw, R.1    Burlingame, A.2    Carr, S.3    Aebersold, R.4
  • 7
    • 0031872701 scopus 로고    scopus 로고
    • Frame: Detection of genomic sequencing errors
    • Brown, N., Sander, C., and Bork, P. 1998. Frame: Detection of genomic sequencing errors. Bioinformatics 14: 367-371.
    • (1998) Bioinformatics , vol.14 , pp. 367-371
    • Brown, N.1    Sander, C.2    Bork, P.3
  • 8
    • 3042735127 scopus 로고    scopus 로고
    • The need for guidelines in publication of peptide and protein identification data: Working group on publication guidelines for peptide and protein identification data
    • Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhskii, A. 2004. The need for guidelines in publication of peptide and protein identification data: Working group on publication guidelines for peptide and protein identification data. Mol. Cell. Proteomics 3: 531-533.
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 531-533
    • Carr, S.1    Aebersold, R.2    Baldwin, M.3    Burlingame, A.4    Clauser, K.5    Nesvizhskii, A.6
  • 11
    • 0027717299 scopus 로고
    • Detecting frame shifts by amino acid sequence comparison
    • Claverie, J. 1993. Detecting frame shifts by amino acid sequence comparison. J. Mol. Biol. 234: 1140-1157.
    • (1993) J. Mol. Biol , vol.234 , pp. 1140-1157
    • Claverie, J.1
  • 12
    • 0022006831 scopus 로고
    • Bacterial peptide chain release factors: Conserved primary structure and possible frameshift regulation of release factor 2
    • Craigen, W., Cook, R., Tate, W., and Caskey, C. 1985. Bacterial peptide chain release factors: Conserved primary structure and possible frameshift regulation of release factor 2. Proc. Natl. Acad. Sci. 82: 3616-3620.
    • (1985) Proc. Natl. Acad. Sci , vol.82 , pp. 3616-3620
    • Craigen, W.1    Cook, R.2    Tate, W.3    Caskey, C.4
  • 14
    • 0035477661 scopus 로고    scopus 로고
    • Bioinformatics and mass spectrometry for microorganism identification: Proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori
    • Demirev, P., Lin, J., Pineda, F., and Fenselau, C. 2001. Bioinformatics and mass spectrometry for microorganism identification: Proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori. Anal. Chem. 73: 4566-4573.
    • (2001) Anal. Chem , vol.73 , pp. 4566-4573
    • Demirev, P.1    Lin, J.2    Pineda, F.3    Fenselau, C.4
  • 15
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.1
  • 16
    • 0035282698 scopus 로고    scopus 로고
    • Prediction of operons in microbial genomes
    • Ermolaeva, M., White, O., and Salzberg, S. 2001. Prediction of operons in microbial genomes. Nucleic Acids Res. 29: 1216-1221.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1216-1221
    • Ermolaeva, M.1    White, O.2    Salzberg, S.3
  • 17
    • 0029870925 scopus 로고    scopus 로고
    • Programmed translational frameshifting
    • Farabaugh, P. 1996. Programmed translational frameshifting. Microbiol. Mol. Biol. Rev. 60: 103-134.
    • (1996) Microbiol. Mol. Biol. Rev , vol.60 , pp. 103-134
    • Farabaugh, P.1
  • 18
    • 33745054329 scopus 로고    scopus 로고
    • Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
    • doi: 10.1186/gb-2006-7-4-r35
    • Fermin, D., Allen, B., Blackwell, T., Menon, R., Adamski, M., Xu, Y., Ulintz, P., Omenn, G., and States, D. 2006. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. 7: R35. doi: 10.1186/gb-2006-7-4-r35.
    • (2006) Genome Biol , vol.7
    • Fermin, D.1    Allen, B.2    Blackwell, T.3    Menon, R.4    Adamski, M.5    Xu, Y.6    Ulintz, P.7    Omenn, G.8    States, D.9
  • 19
    • 0029134925 scopus 로고
    • A frameshift error detection algorithm for DNA sequencing projects
    • Fichant, G. and Quentin, Y. 1995. A frameshift error detection algorithm for DNA sequencing projects. Nucleic Acids Res. 23: 2900-2908.
    • (1995) Nucleic Acids Res , vol.23 , pp. 2900-2908
    • Fichant, G.1    Quentin, Y.2
  • 21
    • 44149105911 scopus 로고    scopus 로고
    • PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites
    • doi: 10.1186/gb-2007-8-11-r250
    • Gnad, F., Ren, S., Cox, J., Olsen, J., Macek, B., Oroshi, M., and Mann, M. 2007. PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol. 8: R250. doi: 10.1186/gb-2007-8-11-r250.
    • (2007) Genome Biol , vol.8
    • Gnad, F.1    Ren, S.2    Cox, J.3    Olsen, J.4    Macek, B.5    Oroshi, M.6    Mann, M.7
  • 22
    • 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., Lipton, M., Edwards, R., Romine, M., Osterman, A., Bafna, V., Smith, R., et al. 2007. Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation. Genome Res. 17: 1362-1377.
    • (2007) Genome Res , vol.17 , pp. 1362-1377
    • Gupta, N.1    Tanner, S.2    Jaitly, N.3    Adkins, J.4    Lipton, M.5    Edwards, R.6    Romine, M.7    Osterman, A.8    Bafna, V.9    Smith, R.10
  • 24
    • 0942287072 scopus 로고    scopus 로고
    • Proteogenomic mapping as a complementary method to perform genome annotation
    • Jaffe, J., Berg, H., and Church, G. 2004. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4: 59-77.
    • (2004) Proteomics , vol.4 , pp. 59-77
    • Jaffe, J.1    Berg, H.2    Church, G.3
  • 25
    • 25444475024 scopus 로고    scopus 로고
    • Genome annotation of Anopheles gambiae using mass spectrometry-derived data
    • doi: 10.1186/1471-2164-6-128
    • Kalume, D., Peri, S., Reddy, R., Zhong, J., Okulate, M., Kumar, N., and Pandey, A. 2005. Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics 6: 128. doi: 10.1186/1471-2164-6-128.
    • (2005) BMC Genomics , vol.6 , pp. 128
    • Kalume, D.1    Peri, S.2    Reddy, R.3    Zhong, J.4    Okulate, M.5    Kumar, N.6    Pandey, A.7
  • 26
    • 12844285613 scopus 로고    scopus 로고
    • Reconstitution of uridine-deletion precleaved RNA editing with two recombinant enzymes
    • Kang, X., Rogers, K., Gao, G., Falick, A., Zhou, S., and Simpson, L. 2005. Reconstitution of uridine-deletion precleaved RNA editing with two recombinant enzymes. Proc. Natl. Acad. Sci. 102: 1017-1022.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 1017-1022
    • Kang, X.1    Rogers, K.2    Gao, G.3    Falick, A.4    Zhou, S.5    Simpson, L.6
  • 27
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.5
  • 29
    • 6344252525 scopus 로고    scopus 로고
    • Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2
    • Liu, S., Milne, G., Kuremsky, J., Fink, G., and Leppla, S. 2004. Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2. Mol. Cell. Biol. 24: 9487-9497.
    • (2004) Mol. Cell. Biol , vol.24 , pp. 9487-9497
    • Liu, S.1    Milne, G.2    Kuremsky, J.3    Fink, G.4    Leppla, S.5
  • 30
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu, P., Vogel, C., Wang, R., Yao, X., and Marcotte, E. 2007. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25: 117-124.
    • (2007) Nat. Biotechnol , vol.25 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.5
  • 31
    • 39749166860 scopus 로고    scopus 로고
    • Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
    • Macek, B., Gnad, F., Soufi, B., Kumar, C., Olsen, J., Mijakovic, I., and Mann, M. 2008. Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell. Proteomics 7: 299-307.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 299-307
    • Macek, B.1    Gnad, F.2    Soufi, B.3    Kumar, C.4    Olsen, J.5    Mijakovic, I.6    Mann, M.7
  • 33
    • 0345685440 scopus 로고    scopus 로고
    • Detecting and analyzing DNA sequencing errors: Toward a higher quality of the Bacillus subtilis genome sequence
    • Medigue, C., Rose, M., Viari, A., and Danchin, A. 1999. Detecting and analyzing DNA sequencing errors: Toward a higher quality of the Bacillus subtilis genome sequence. Genome Res. 9: 1116-1127.
    • (1999) Genome Res , vol.9 , pp. 1116-1127
    • Medigue, C.1    Rose, M.2    Viari, A.3    Danchin, A.4
  • 34
    • 0018862384 scopus 로고
    • Post-translational modification of elongation factor 2 in diphtheria-toxin-resistant mutants of CHO-K1 cells
    • Moehring, J., Moehring, T., and Danley, D. 1980. Post-translational modification of elongation factor 2 in diphtheria-toxin-resistant mutants of CHO-K1 cells. Proc. Natl. Acad. Sci. 77: 1010-1014.
    • (1980) Proc. Natl. Acad. Sci , vol.77 , pp. 1010-1014
    • Moehring, J.1    Moehring, T.2    Danley, D.3
  • 35
    • 0036419051 scopus 로고    scopus 로고
    • Breathing metals as a way of life: Geobiology in action
    • Nealson, K., Belz, A., and McKee, B. 2002. Breathing metals as a way of life: Geobiology in action. Antonie Van Leeuwenhoek 81: 215-222.
    • (2002) Antonie Van Leeuwenhoek , vol.81 , pp. 215-222
    • Nealson, K.1    Belz, A.2    McKee, B.3
  • 36
    • 33846010726 scopus 로고    scopus 로고
    • Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics
    • Nielsen, M., Savitski, M., and Zubarev, R. 2006. Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics. Mol. Cell. Proteomics 5: 2384-2391.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 2384-2391
    • Nielsen, M.1    Savitski, M.2    Zubarev, R.3
  • 38
    • 0026590172 scopus 로고
    • Finding errors in DNA sequences
    • Posfai, J. and Roberts, R. 1992. Finding errors in DNA sequences. Proc. Natl. Acad. Sci. 89: 4698-4702.
    • (1992) Proc. Natl. Acad. Sci , vol.89 , pp. 4698-4702
    • Posfai, J.1    Roberts, R.2
  • 39
    • 13944268797 scopus 로고    scopus 로고
    • A novel method for accurate operon predictions in all sequenced prokaryotes
    • Price, M., Huang, K., Alm, E., and Arkin, A. 2005. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 33: 880-892.
    • (2005) Nucleic Acids Res , vol.33 , pp. 880-892
    • Price, M.1    Huang, K.2    Alm, E.3    Arkin, A.4
  • 40
    • 1842681979 scopus 로고    scopus 로고
    • Standard mixtures for proteome studies
    • Purvine, S., Picone, A., and Kolker, E. 2004. Standard mixtures for proteome studies. OMICS 8: 79-92.
    • (2004) OMICS , vol.8 , pp. 79-92
    • Purvine, S.1    Picone, A.2    Kolker, E.3
  • 41
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm, M., Storm, C., and Sonnhammer, E. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314: 1041-1052.
    • (2001) J. Mol. Biol , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.2    Sonnhammer, E.3
  • 44
    • 33646903914 scopus 로고    scopus 로고
    • Modificomb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures
    • Savitski, M., Nielsen, M., and Zubarev, R. 2006. Modificomb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol. Cell. Proteomics 5: 935-948.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 935-948
    • Savitski, M.1    Nielsen, M.2    Zubarev, R.3
  • 45
    • 33747885134 scopus 로고    scopus 로고
    • A computational approach toward label-free protein quantification using predicted peptide detectability
    • doi: 10.1093/bioinformatics/btl237
    • Tang, H., Arnold, R., Alves, P., Xun, Z., Clemmer, D., Novotny, M., Reilly, J., and Rejivojac, P. 2006. A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 22: e481-e488. doi: 10.1093/bioinformatics/btl237.
    • (2006) Bioinformatics , vol.22
    • Tang, H.1    Arnold, R.2    Alves, P.3    Xun, Z.4    Clemmer, D.5    Novotny, M.6    Reilly, J.7    Rejivojac, P.8
  • 46
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra
    • Tanner, S., Shu, H., Frank, A., Wang, L., Zandi, E., Mumby, M., Pevzner, P., and Bafna, V. 2005. InsPecT: Fast and accurate identification of post-translationally 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.4    Zandi, E.5    Mumby, M.6    Pevzner, P.7    Bafna, V.8
  • 48
    • 39749149149 scopus 로고    scopus 로고
    • Systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: The response of Shewanella oneidensis to chromate exposure
    • Thompson, M., Thompson, D., and Hettich, R. 2008. Systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: The response of Shewanella oneidensis to chromate exposure. J. Proteome Res. 7: 648-658.
    • (2008) J. Proteome Res , vol.7 , pp. 648-658
    • Thompson, M.1    Thompson, D.2    Hettich, R.3
  • 50
    • 28644447919 scopus 로고    scopus 로고
    • Identification of post-translational modifications via blind search of mass spectra
    • Tsur, D., Tanner, S., Zandi, E., Bafna, V., and Pevzner, P. 2005. Identification of post-translational modifications via 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.5
  • 51
    • 0026733573 scopus 로고
    • Ribosomal movement impeded at a pseudoknot required for frameshifting
    • Tu, C., Tzeng, T., and Bruenn, J. 1992. Ribosomal movement impeded at a pseudoknot required for frameshifting. Proc. Natl. Acad. Sci. 89: 8636-8640.
    • (1992) Proc. Natl. Acad. Sci , vol.89 , pp. 8636-8640
    • Tu, C.1    Tzeng, T.2    Bruenn, J.3
  • 52
    • 0019333178 scopus 로고
    • ADP-ribosylation of elongation factor 2 by diphtheria toxin. NMR spectra and proposed structures of ribosyl-diphthamide and its hydrolysis products
    • Van Ness, B., Howard, J., and Bodley, J. 1980. ADP-ribosylation of elongation factor 2 by diphtheria toxin. NMR spectra and proposed structures of ribosyl-diphthamide and its hydrolysis products. J. Biol. Chem. 255: 10710-10716.
    • (1980) J. Biol. Chem , vol.255 , pp. 10710-10716
    • Van Ness, B.1    Howard, J.2    Bodley, J.3
  • 53
    • 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., and Marcotte, E. 2005. Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias. Genome Res. 15: 1118-1126.
    • (2005) Genome Res , vol.15 , pp. 1118-1126
    • Wang, R.1    Prince, J.2    Marcotte, E.3
  • 54
    • 0012252011 scopus 로고    scopus 로고
    • Full subunit coverage liquid chromatography electrospray ionization mass spectrometry (LCMS+) of an oligomeric membrane protein: Cytochrome b6f complex from spinach and the cyanobacterium Mastigocladus laminosus
    • Whitelegge, J., Zhang, H., Aguilera, R., Taylor, R., and Cramer, W. 2002. Full subunit coverage liquid chromatography electrospray ionization mass spectrometry (LCMS+) of an oligomeric membrane protein: Cytochrome b6f complex from spinach and the cyanobacterium Mastigocladus laminosus. Mol. Cell. Proteomics 1: 816-827.
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 816-827
    • Whitelegge, J.1    Zhang, H.2    Aguilera, R.3    Taylor, R.4    Cramer, W.5
  • 55
    • 33750142707 scopus 로고    scopus 로고
    • Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: Does deamidation contribute to crystallin insolubility?
    • Wilmarth, P., Tanner, S., Dasari, S., Nagalla, S., Riviere, M., Bafna, V., Pevzner, P., and David, L. 2006. Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: Does deamidation contribute to crystallin insolubility? J. Proteome Res. 5: 2554-2566.
    • (2006) J. Proteome Res , vol.5 , pp. 2554-2566
    • Wilmarth, P.1    Tanner, S.2    Dasari, S.3    Nagalla, S.4    Riviere, M.5    Bafna, V.6    Pevzner, P.7    David, L.8
  • 56
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
    • Xie, X., Lu, J., Kulbokas, E., Golub, T., Mootha, V., Lindblad-Toh, K., Lander, E., and Kellis, M. 2005. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.3    Golub, T.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.7    Kellis, M.8


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